(DISCONTINUED) Evangelion:We Can(And Will)Reverse This
by KnightOfZ3R0
Summary: Shinji Ikari wakes up to a world unlike the one he once knew: NERV is lost to time, Misato commands Anti-NERV Force WILLE, and Shiro is nowhere to be found with hints of his disappearance pointing to the organization dubbed NEVEC. It's now up to Shinji and the friends he makes along the way to fix his past, and uncover the truth about SEELE and the Human Instrumentality Project.
1. Chapter 1

_**Neon Genesis Evangelion, the End of Evangelion, and the Rebuild of Evangelion are owned by Hideaki Anno and written by Yoshiyuki Sadamoto. I own no elements from the original Manga, TV show, or Rebuild and EOE films but my OC's.**_

 _ **That said, Please Enjoy The Show!**_

* * *

 **Chapter 1: The Devil's Return**

 **Earth, high atmosphere**

" _Pursuit Squadron, report both EVA's current positions."_

" _Pod 02-Dash has now reached operable altitude. Now in the targets orbit."_

" _And Pod 08?"_

" _Experience problems in orbit due to lack of altitude, will be in operable range shortly."_

" _Understood. 02-Dash will have to solo this operation then."_

" _Acknowledged. Pod 08 will as supporter here on out."_

" _Transition from shift to seven."_

" _Pod 02-Dash now passed point of no return."_

" _And NEOS?"_

" _They haven't noticed the Pods, ma'am. We should be safe with the Akrid they're dealing with as long as they don't send out any drones or Evas."_

" _Let's hope so… Otherwise we'll be dealing with NEVEC or Akrid, would be a hell of a lot worse….."_

" _Pod 02-Dash entering Area 88!"_

" _Roger. Operation US is a go!"_

" _Understood, Pod 02-Dash now entering final operational orbit."_

" _Now transferring to deceleration."_

" _Turning RCS, confirmed activation."_

" _Stage one, engine ignite!"_

" _No problems in posture-control system."_

"Combustion initializing." High above Earth, in the beautiful infinite black sky of stars and dots of white, a single star-like object of metal proportions came to life with powerful engine cells. If pushed higher and higher, before finally the engines faded as the object found itself floating completely in the silence. _"S1C combustion a success!"_

" _Contact ring is now ready for separation."_

More voices rose with speed as the star split apart, four of the points leaving the body as triangles with flashing points. The metal pieces steadily hovered away from the remaining body, which split from its second half and roared to life with engines once more. Once more voices spoke reading success or other layouts in the Operation as more parts detached form the whole.

A pair of large triangular objects hovered along, held together by a center point which seemingly was designed as a shield or body of a shuttle. The triangular sides had large engines at their ends, the whole painted gun metal grey with red outlining holding the machinery together. The object began rising, before slowly descending back to the blood red form of Earth, clouds hovering softly as the object stuck out above the surface. Its pilot watched through her red helmet, eyes studying the area as the holographic readouts on the Entry Plug's sides read out to her. _"Unit is on intercept course with target package."_ A voice rang out through the Plug, making the pilot grip the controls tighter. _"Eighty measures till contact."_

" _Confirm the target."_

" _Contract point is unchanged."_

" _Maintaining Shift-M, no casualties."_

" _02-Dash, prepare for rendezvous point."_ The radio rang once more as the pilot of 02-Dash began readying her grip, flexing her fingers and the controls of her 'weapon.' _"08's lacking altitude, so it'll only be able to assist for 96 seconds before re-entry. So finish this fast."_

" _Reflective waves detected in targets space."_

" _NEVEC?"_

" _No, not Evas or the NEOS Station. They're jamming us however!"_

" _More than likely NEOS's auto-defense system array."_ Bullets of light flashed passed Pod 02-Dash as it hovered across the darkness. _"Don't worry, I ain't alone, meow."_

The bullets flew by before a wave of explosion surrounded Pod 02. _"Burst shockwaves detected! Contact in three… two….!"_

Pod 02's pilot shuttered as its A.T Field lite up, the explosions sending waves of power through the Plug. _"Second wave incoming: it's a Pattern Blue."_

" _Troublesome bunch eh?"_

" _Approaching object identified…. Confirmed, it's the Mark.04-A."_

The object moved with speed faster than that of a jet, it's 'A.T Field' acting like a thrust which helped it slam into Pod 02's Field. The Mark.04-A was not much to say: a generic grey disc with small purple wings sticking out the top with yellow lightings, and two pairs of fast moving needle-like legs that tried cutting through the A.T Field.

" _Crap, it's an Anti-A.T Field!"_ The pilot cried out, watching as the Field's began nullified long enough for the legs to cut through. The legs forced away the Field and revealed several inner cannons which fired at Pod 02. The shields of Pod 02 came to life, blocking out the bullets before finally giving way. _"Damnit, half this crap is useless!"_

The shield was ripped away from the 'Pod' itself, revealing an Ex-NERV Evangelion, more specifically Evangelion Unit-02 Dash. The Eva still held its red, black, white and yellow colors, with several oranges spots on the head crest just above the repaired right eyes. Its whole left arm was replaced with a bulky gatling gun like weapon, black and red to match the new shoulder pylons.

" _And this stupid helmet has to go!"_ The pilot gripped the helmet, ripping it off completely to reveal Asuka Langley Shikinami, left eye covered by an eye patch yet still holding her orange hair and glaring blue eye. "How the hell Shiro used these damn things in combat is something he took to the grave with him! And Network Four-Eyes, stop that damn singing! It's pissing me off!"

Unit-02 Dash's A.T Field rose fast and on time, as Mark.04-A slammed its legs into the Field. It forced the EVA back before its shot away, exploding into a ball of fire. "Support was 2 seconds late!" She snapped, glaring down to her supporter. Lower down was another Evangelion, EVA Unit-08. This EVA, unlike Unit-02 stood out more with a light pink color scheme, with white, green and yellow add on lines and topped off with a eight green-eyed helmet.

" _And_ you _were three seconds before final position."_ The pilot claimed with a cocky tone, grinning under her own blue and pink helmet. _"It's called adaptation, Princess. Try and keep up with me!"_

Unit-08 sat without its engine cells, shields covering its form as its snipe rifle stood out like an antenna. Mark0.04-A's attempted to assault Unit-02 Dash as it continued forward, exploding before the Nemesis Series drones could get close enough. "Just passed the Fullerene Shift, now entering Final Defense Area 89." Asuka reported, blinking as the target drew closer to Earth and herself. "Target's on the move!"

The 'target' as called was a large metal cross like cage, with four box arms sticking all directions as it slowly descended. "No time to correct orbit!" Asuka yelled out, pulling up as she shot out several couplings at the target from her grapple cannon-arm. "I'll have to brute this!"

Unit-02 Dash went sailing past the target, but the cross held firm to the zero gravity like an anchor as it pull the EVA back fast. The Ex- Second Child glared up and reeled the grapples, pulling her towards the cross object. Both the EVA and cross object came into contact with the engine cells on Unit-02 Dash snapping into place with a roar of power.

The engine flared harsh as they forced the EVA and target object back into orbit, letting Asuka sigh in slight relieve. "Combustion terminated." She called out, looking to see the booster cells detach from her Unit-02 D's shield and fly out into space. She heaved in air, glaring to her side. "Target successfully captured. Returning to base."

" _Roger, we'll be waiting at the retrieval point."_ A voice called from the radio. _"Callout sign is Saturn VI."_

"Roger." An alarm blared once more, and Asuka looked to see a Pattern Analysis screen come to life. The Analysis was Blood Type Blue. "The hell?! Another Pattern Blue, where the hell is it?!"

Unit-02 looked from to side, but failed to see the drone reveal itself from underneath the cross. Or above it….? The box sides opened, letting them sail out more to form 2 familiar designed pairs of thin, metal paper like arms. "Object is identified as a Mark.04-B! It's deploying field-reflective coating!" Asuka yelled out, glaring with annoyance. "And so close to a successful re-entry, the cunts…. Network Four-Eyes, I need support!"

" _Nope, no can do!"_ Unit-08's pilot yelled out, releasing its rifle and kicking off the shield cover to give a final wave as she descended. _"Have phun! See you at the surface!"_

"God, you are so useless!" Asuka screamed in anger, pulling her EVA under the target object and proceeding to kick it away. She failed though, as the drone kept a firm grip to the cross. "No one told me about this when I signed up!"

The metal arm like tethers fixed themselves into the center, finally becoming a large halo which shined brightly above the pair. Asuka's eye widened, and a faint echoing noise found its way to her ears and eyepatch. She gripped her now light blue flashing eye cover tightly, trying to look away from the light that surround Unit-02 Dash. "Damnit, what's with the light?!" She cried out, her EVA trying to look away as the light pulsed more around its head. "My A.T Field isn't neutralizing it!"

"I have to kill that damn core block!" She stated, before glaring with a frown as she saw the core began rushing up one of the tendril arms. "And just when I speak…. Where are you going?!"

Light flared all around her EVA and the object as the operation was seemingly giving away, with the LCL in the Entry Plug burning more and more. "Damnit, I can't maintain my altitude angle!" She cried out in realization, watching as her EVA continuously spiraled downward. "My EVA's going to collapse!"

" _02-Dash, capture of Evangelion Unit-01 is top priority!"_ The voice of her superior on the radio yelled out, making her growl. _"Do not let that damn EVA go, even if Unit-02 is lost!"_

"No shit it's the priority!" Asuka yelled out through the alarms and LCL bubble, glaring at the "SOUND ONLY" communication screen. Unit-02 pulled itself up, before the Mark.04-B fired a beam which tore off the EVA's left arm. Asuka screamed through the pain with more explosions following close, her eye landing on the coffin which housed the person she once called 'friend.' "Why don't you help me out huh?! Stupid fucking Shinji!"

Then, as if God or Shinji himself seemed to answer her prayers, Asuka got one hell of a response.

The coffin side exploded with a crack which shed a red glow. From out of the crack crackled a beam of raw power, which cut apart the many halo rings around Asuka's EVA and the coffin. The rings exploded apart as the beam followed the Mark.04-B drone, burning apart the tendril it road on before cutting the drone itself. An explosion of energy ensued, leaving a now wondering and confusion Asuka to stare at the glowing eye of Unit-01.

For a moment, she swore it wasn't the Evangelion Unit-01 she fought with during the Angel War. No, it felt human and familiar…. It felt like she was having a silent, only eye conversation with Shinji, the _real_ Shinji Ikari.

She could feel the emotions mixed in her chest swelling up at the sight of it, and while she tried to hide them it was clear all across her face.

She watched finally as the eye seemed to water slightly, as it in joy, surprise or fear, before it closed, leaving her alone. "….. Idiot….." She muttered, looking down to their home with a slightly saddened look as her EVA and Unit-01's coffin began re-entering Earth's atmosphere.

* * *

As it did, now far hovered a large asteroid like structure, with a large building in the center with several towers poking out above and a large cannon underneath. Explosions occurred all across it as machine cannons and shielding came back. _"This is NEOS Station reporting in to Stormbreaker. WILLE and NERV Jump Drones had been dealt with. Evangelion Unit-01 has entered WILLE's airspace, no chance of recovery over."_

" _Roger, this is Unit-10 at Stormbreaker HQ. Continue monitor of AAA Wunder and fleet till further notice."_

" _Understo-."_

" _Unidentified object in northeast sector! It's moving towards us!"_

" _Pattern Yellow: it's an Akrid!"_

" _What the-?!"_ NEOS weaponry came to life once more, beams of light rushing out with bullets following to hit the object. The object, or rather creature, roared across the whole of the station and Earth, going right through the station rock and hull with a fiery explosion all across the right side. The creature's armor tough skin shinned across the fire and sunlight, rushing downwards with another echo of demonic feat. _"Damn it, this is NEOS reporting in again! We have an unidentified Cat-G Akrid moving towards Earth, its moving at rapid speeds! We attempted to intercept but its rammed right through us! It may be heading to your location, over."_

" _Must have sensed the Thermal Energy we're loading….. Acknowledged, we're moving out. Maintain current watch and repair NEOS as soon as possible."_

" _Understood. NEOS, out."_

* * *

On the surface, staring up into the dark night, a young boy watched with interest as he saw Unit-01 began entering Earth's atmosphere. He smiled; he felt his friend's older brother pulse with power not far, which only helped to confirm his knowledge of the coming times. "Welcome home, Shinji Ikari." Kaworu Nagisa spoke aloud, smiling as he stared to his future friend before turning his head back. "We've been waiting for you…."

In a lone chamber, silent yet alive, a lone person slept. He'd slept for so long in waiting he hadn't known when or where he was, all he knew was he'd felt _it_. Something he never thought he'd feel again. _"Shinji…."_ The name echoed through its 'home'. _"Shinji, I….._

 _I've missed you, brother…."_

* * *

 ** _A/N: Yes, the rumors are true: I am alive! And I'm back to write the sequel to Evangelion: You Are(Not)Null. Sadly, I won't be able to keep uploading chapters every three days like before as my STAAR testing is coming up next week and I'm going to be working my butt off to pass, so wish me luck if the next chapter comes up next friday! Now I don't have a specific time for uploading just yet with tests and all, so I will try and squeeze time into making new chapters for possibly every weekend or every 2 weeks so yeah..._**

 ** _That said, this is the KnightOfZ3R0 signing off!_**


	2. Chapter 2

_**Neon Genesis Evangelion, the End of Evangelion, and the Rebuild of Evangelion are owned by Hideaki Anno and written by Yoshiyuki Sadamoto. I own no elements from the original Manga, TV show, or Rebuild and EOE films but my OC's.**_

 _ **That said, Please Enjoy The Show!**_

* * *

Talking-"Hello"  
Radio/EVA Voice- _"Hello"  
_ Thoughts- _Hello  
_ VEELE/Clones- _ **"Hello"  
**_ A.I- **"Hello"**

* * *

 **Chapter 2: Wake Up Call**

" _I've missed you…. Brother….."_

Shinji awoke for the first time in a _long_ time with a gasp and jolt, bumping his head hard. "Ach!" He cried out, trying to pull his arm up. He felt cold metal around his wrists, glancing to his side to see "Unfamiliar ceiling again… Wait… Table cuffs….? What the….?"

He looked forward to see a glass screen before him, barely able to make out a far ceiling in the red chamber.

After what felt like hours he found himself on a surgery gurney, hands cuffed to the metal table with a holographic like screen above his head. "Cardiopulmonary function is normal," a female voice spoke out, teenage much to Shinji's slight dismay. He'd been hoping for an adult to speak up in the-what he assumed to be-elevator, explain just what the hell was going on and why there were guards pointing guard as _him_. "No palsy of extremities are discernible. Yes, he's opened his eyes."

A face came up before him, looking down at his slightly confused look. The face was young and a female at that, though she felt very familiar to look at. She also wore a hat by the looks of it, but he didn't look to see the symbol on it as she continued. "Do you understand what I'm saying?" she asked, coming away as he followed her with his eyes.

He raised an eyebrow, before finally looking around. "Um, where am I if I may ask?" Shinji blinked, not realizing his voice for a moment. It sounded deeper…. More mature, more…. "I sound… Older?"

"Good, he's able to talk." The girl stated, a hand to an earpiece he couldn't make out from under her hand. "Consciousness has returned to BM-03."

"W-Where am I?" He asked with slight confusion, blinking as slight memories came back. The Geo-Front exposed, the Tenth Angel destroying Null Unit and Unit-02, Unit-01 trying to fight it, and then him and Rei floating in an Entry Plug …. "Wasn't I just in Unit-01 with...Rei?"

"Yes, ma'am. His memories seem to be returning." The girl stated, looking to him with a concerned look.

"W-Where's Rei…?" He asked, though the girl nor did the troops reply as she looked back to his face.

"Tell me, do you know who this person is?" Her face vanished as Shinji's face appeared, and he recoiled fast enough to his head on the metal.

"Ow! That hurt…." He groaned, blinking before he looked back to his reflection. "Is that… Me? Jesus I look… Huh, I look the same?"

Nothing seemed to have changed drastically aside from Shinji's hair, which was slightly longer, ending just below his shoulders. Though his face and voice was the same, the same Child that'd fought with NERV. "He can recognize himself. No apparent problem, ma'am." She continued, the reflection vanishing.

"What… The hell is that thing on my neck?" He'd managed to get a glance of whatever it was around his neck, it appeared to be a collar with a red square in the center with a black line going through it. "I… Didn't know the army was enlisting that sort of stuff into the military attire now…"

The girl gave a slight giggle before pushing it away, mostly due to the troops glaring to her. "Do you have to urinate? Or are you hungry?" She asked, though Shinji seemed to have little say in even that at the moment.

"U-Um, no. No miss, I do not…." He replied, sighing as he felt the elevator they rode stop. "I'm guessing we've arrived somewhere important….?"

* * *

 **Command deck, unknown location**

He got his answer once they'd rolled him to a door which rushed open. Before sat a plethora of wire connecting from the ceiling to whatever was in front of them. At the far end were several large red openings in the shape of circles.

"Delivery clearance is up to 86%."

" _Maintain N2 Reactor power generation to 90%..."_

"No NEVEC or NERV cruisers defected within the twelve hundred radius."

"Open the pressure valves manually…."

"No flying objects discernible."

"Don't worry about the condenser…."

" _Prioritize the Black D battleships to transferring personnel."_

"We need more people to bring up the rations!"

"….Hurry it up then!"

"Checking the gyro compasses of ships 3 & 5."

"Gauge is inaccurate. Requesting calibration."

" _Outfitting all ships. Checking the road-map."_

"Armament work is at 3% behind schedule."

"Ma'am, we've brought Specimen BM-03!" The girl stated, the gurney Shinji rested on stopping next to a high command platform surrounded by metal railings. On the platform stood alone figure with another by a machine on the other side, feminine from the phrase "ma'am" which had been thrown around by the girl. She wore a red jacket like attire with black pants, and a red captain like cap to finish it off.

"Excellent," the woman stated, the familiar emotionless tone Shinji had grown familiar with edged into her voice. "Release him. The rest of you may all go."

Immediately the large cuff holders on the gurney unlocked, the troops slowly walking away as Shinji rose up with a groan.

"Recheck all ship steering equipment. No problems noticeable." Shinji blinked, looking around. _That voice,_ he thought to himself. _Is that… Makoto Hyuga?_ He didn't feel like notice it at first, but he slowly began to realize everything went silent aside from the radio buzzing as everyone stared silently.

More specifically at him. "Oh, God…. I'm going to get jumped…." He whispered to himself, looking around before up to the-what he assumed- captain or commander. "Wait…. Is that…. Misato?"

"Shinji Ikari." Shinji blinked at the voice; it was definitely Misato. Something was off though, she sounded more like his father, like some sort of robot rather than herself. " _Can_ I call him that?"

"I suppose." Another voice came familiar to him, he found it to be Ritsuko Akagi's, NERV's Project Evangelion overseer. "His physiological data matches the Code 03 Boy. His dental profile and body compositions are 100% identical to the Near-Third Impact incident."

"Though the results of his Deep Level Synchronization tests are currently being analyzed." Captain Katsuragi clanked to her side, looking down at 'Shinji.' She didn't want to say it anymore, the words she'd held onto so long ago then. Or better yet, she didn't feel the need to. Not after the _other_ incidents….

"And the DSS Choker on his neck?" She asked her friend/second-in-command.

"Already installed on him, Captain Katsuragi." Ritsuko finally turned to face her friend, her hair no longer spread out or long as it was cut short, though she still kept her makeup and ear pieces.

"Captain Katsuragi? I could have sworn you were a Colonel….?" He whispered, before it finally dawned on him. "You really are Misato Katsuragi…."

A sudden beep caught his attention from his neck, making him blink with worry and touch his collar piece. Ritsuko now held a device similar to a revolver grip and trigger, though it didn't have a gun barrel and had a red sphere at the back. She looked to the circular end point on the grip, which created a hologram that was too far for Shinji to make out. "It's functioning at full power, and I've had it set to your personal pass code, Capt."

"Alright." Cap. Katsuragi took the trigger from Ritsuko, looking down at it with a glare under her visor like sunglasses. _Once more, you old tool_ she thought to herself _. Another few years, another twisted reflection of our past failures._

"The hell is this thing?" Shinji asked slightly louder, tugging at his collar piece, or the 'DSS Choker' as Ritsuko and Misato dubbed it. "Damn it, come off!"

Definitely Shinji, Misato thought once more with a barely noticeable pint of humor. None of the others cursed like him. Stupid fucking goody-two shoes clones….

"T-There is no way to take it off." The girl explained, looking up with affect. "Or rather, there's no way _we'll_ take it off."

"We're done here, with him." Cap. Katsuragi stated, turning around and back to the bridge like set up. "Take him up to quarantine."

The familiar red hexagon warning and holographic images came up at the front. "Decoys-01 and 05 have been obliterated." Another voice, Shigeru Aoba in particular, spoke up from one of the seats. "Wavelength has been detected!"

"Huh, what's this?" Another voice spoke up, this one new. It came from another female technician, with pink hair who sounded like she just started working at NERV.

"Akrid?" Cap. Katsuragi raised her head up slightly, slight fear at the tip of her tongue.

"Negative on that Captain, it's a Pattern Blue!" Makoto yelled out, glaring down to the technician. He sighed, looking back to his superior. "Targets have been identified; Nemesis Series, Cap!"

"Damn, they're here." Cap. Katsuragi responded not in fear, but rather annoyance.

" _They're attacks are three-dimensional!"_

"Targets are identified as Mark.04-C's, ma'am." Ritsuko stated, looking to her superior. "They want to lock us here. But we can't leave just yet-"

"Stop working on everything _but_ the main engine." Cap. Katsuragi interrupted, crossing her arms as she studied the situation before them. "All ships, Battle Station Level 2! Target all Nemesis Series!"

"Roger." Another screen came up, this time a hexagon longer, as it read: All Stations: CONDITION II. "All ships, the Battle Stations 2. Prepare for aerial, sea or underwater assault and confrontation!"

"Abandon all transfer of supplies." Shigeru pulled up a phone, throwing in orders at the person on the opposite side. "Yes, prioritize transfer of personnel!"

* * *

 **Northern epicenter, Arctic Circle**

"All ships abandon supply transfer and prioritize personnel transfer!" Across the freezing Arctic, a large fleet of naval warships sat around a larger vessel in the red sea. The vessel was huge, dwarfing even the Naval Aircraft-Carrier Over the Rainbow.

It was red, wither several large with three parabolic dishes on the top. Across its worm were several large stations with large cranes, moving parts and pieces all around the form of its hull.

" _Continue work on the main engine!"_

" _I repeat, prepare for aerial, sea or underwater assault and confrontation!"_ Makoto's voice repeated, alarms now blaring as ships began readying their cannons. _"Prepare for long-range cannon ray assault!"_

" _Confirm the opening state of all power supply lines."_ Helicopters rushed into the air, with large crates and machines being pulled fast through the blizzard. _"All aircraft, leave current airspace now! Head to meeting Point 02 with all haste."_

" _Abandon all remaining cargo! Personnel transfer is now top priority!"_

" _Continue ship outfitting!"_

" _Keep working, even to the last second!"_

" _All those who can help the power lines, assemble at the utility boat immediately!"_

" _All cannon towers, prepare for assault."_ Without haste, Navy destroyer cannons rushed to turn, aiming high and trigger fearful at the attack _. "Activate all remote control linkage systems. Be ready for any surprise attacks!""_

"Keep working on the injection for the main engine transfer system." A technician ordered, moving on the control console he stood at.

" _Hurry!"_

" _Understood, N2 Reactor is now functioning at 99% output!"_

" _Working on injection!"_

" _Now opening 1_ _st_ _90 valves."_

" _Lower power pipes now connected!"_ On the Over the Rainbow carrier, hundreds of large power cables ran off the deck and onto the large vessel, warm with power as more orders were yelled out _. "No irregularities in 3_ _rd_ _or 4_ _th_ _Hub Stations to port!"_

" _Roger, opening all 1_ _st_ _90 valves."_

" _Beginning energy supply."_

" _Power supply to N2 Reactor now going smoothly."_

" _Inspecting LCL Circulation Pumps."_ Deep in the vessel, the familiar Unit-08 laid in a bath of red LCL with large machine and pipes around it. _"Checking all filtering systems."_

"All right, Battle Stations everyone!" Another familiar voice, specifically Maya Ibuki, spoke up with pure authority as she and others stared outside. "Take positions immediately! You there, move it now!"

"No dice, it isn't working Chief!"

"This is what we get for having a motley crew with civilians working." Another technician groaned, making Maya turn with a glare.

"That's no excuse! Back to work!" She barked, glaring with hands to her hips. A lot had changed, and she did not plan to be the same sly little girl she was back at NERV since then. She tsked, glaring away with a snarl. "This is why I hate newbies, especially younger men…."

* * *

 _Jesus, these people are doing horrible with planning this,_ Shinji thought with sadness as he watched people work with manuals. "Let's see," another technician spoke up, looking from his screen back to the manual fast. "Stop the outfitting here…. Start closure of barrier walls…. Is this is?"

"Watch the skies carefully," The pink haired technician spoke to herself, much to Shinji and Shigeru's unknowing concern. "And here's sonar direction…."

"Kitakami!" the Ex-NERV technician called out, glaring to the newbie in front of him. "What's upper decks status?"

"Wait, I'm in charge of that?" Midori Kitakami asked, looking up at the frustrated glare of Shigeru.

"Yes, you dummy! We all have _double_ jobs!" Ritsuko couldn't help but sigh silently. Oh how much she missed the organized and perfect command structure of NERV technicians, now she had to deal with complaints and the many groans everywhere she went.

"Seriously?"

Shinji groaned. "Jesus, NERV let itself go bad…." He muttered silently, looking to the girl from earlier as she looked under a flight of stairs. He pondered on who she was, and just why she felt so familiar to him. He also wondered where he was, and if NERV was still fighting the Angels since then. _It they are, they're doing a piss poor job then…._

"You know it's dangerous to be standing while we move. You should stay here." She exclaimed, point to the area as more radio voices came up.

" _AA cannons and guided missiles ready on all cruisers and ships!"_

"I hate to say it but there's so much tension around the bridge during Battle Stations!" The girl exclaimed cracking her back as she looked up to the Captain.

"Good," Cap. Katsuragi replied, watching the holographic video link the battle showed. "Link all AA systems together. Protecting EVA Unit-01 is our top priority."

"U-Unit-01?" Shinji blinked with surprise, shocked to hear the familiar call sign of his Evangelion. _If it's here then Rei is definitely here!_ He thought silently before he was pulled out of his thoughts.

"They're here!" Kitakami called out, her radar screen flashing with multiple targets enclosing the area. "Pillars of Light from targets confirmed! Numbers are increasing!"

"Identification of target Core blocks are impossible!"

"Must be hiding in a cloaking cocoon." Ritsuko thought aloud. "That is a problem, at this rate we'll be sitting ducks in the saturation attack."

" _600 seconds till contact!"_

"Captain Katsuragi, I advise we spread the fleet out immediately." Ritsuko continued, looking to her superior once more, who simply stared forward in silence. "We have insufficient and unskilled personnel, and our ship is still in the process of being outfit for flight. Worst of all, we're unable to identify the targets Core blocks. Our chances of victory in a sense are 00.00%."

"We have no choice but to retreat, Captain!" Ritsuko finally exclaimed, hoping to get a raise from her friend. She got nothing, just the silence which reminded her so much of the bastard Gendo Ikari.

Cap. Katsuragi finally looked slightly up, glaring under her shades. "All the more reason to change the situation and get rid of all anxieties in the future." She reasoned. "From this point on we're _flying_ , Vice-Captain."

"Flying?!" Ritsuko blinked, before realizing just what Misato meant. "You aren't serious about using the main engine?!"

"All cruisers and stations, prepare for launch!" Cap. Katsuragi ignored her Vice-Captains exclaim of fear, glaring forward with the order. "Prepare to ignite the main engine!"

"What?!" Everyone turned with fear to the Captain. Never had they tried to use the main engine, not even during the MB-01 and 02 incidents. No the Captain wanted to use it, even with the risk of killing every one of them?!

"That's insane, we can't use this ship in battle Captain!" Ritsuko tried to reason, fearful of her friend's insane idea.

"I agree!" Another technician cried out, looking up to the emotionless commander of their force. To use the engine was suicide, even with complete power and a powerful energy supply. "We haven't performed a single test flight let alone a VR simulation of one, it's too dangerous!"

"And I have no experience in Gravity control." Another cried out, looking up with fear. "I don't think I can do it!"

"I-I'd rather not fight a battle we'll lose!" Kitakami retorted. "I don't' want to die in a fight we'll lose!"

"Oh you'll die when the time comes, it's that simple!" Another technician growled out, looking to his pink haired companion behind himself. "You younglings really need to stop complaining so damn much…."

"Excuse me, but aren't you a bit too old to say that?!" Kitakami snapped, glaring at the man who returned the glare nervously. The last thing they needed was a fight at a time like this. "Shouldn't you be watching out for yourself?"

Tension rose more and more, the older fighting with the old. But this was not the place or time, especially with others outside in the fight! They needed to act, not fight anymore! _This is getting us nowhere,_ Katsuragi thought to herself.

"Yes, I admit it is insane." Cap. Katsuragi finally stated, fixing her hair slightly as she continued. "But we aren't going to fight! We'll simply use our ships to bait the enemy targets out!"

"The power to kill God, huh?" Ritsuko asked, sighing before looking back to the control console. "I'll see what I can do. But I should remind you the ignition systems haven't been installed. That is…. Unless you plan to use EVA?!"

Katsuragi didn't reply, but she did take up a radio and spoke with haste. "Mari?"

" _Unit-08 isn't ready yet!"_ Came the reply. _Oh great, she's here_ Shinji thought with a shiver. _I really need to ask her about being connected to my family. Maybe she knows something I-_

"And Asuka?"

"Asuka?" Shinji blinked, looking up sharply at Katsuragi when she said the name. "Sh-She's here too?!"

" _I'm already on it!"_ came the answer, the familiar voice of the Second Child rushing to Shinji's ears. He felt time freeze and his heart stopped. _"I just have to fix the igniter into the engine right?"_

"Yeah, I'm counting on you." The Captain encouraged, before she continued. "But you should know there is a barrier density situation around the engine."

" _And no one's working on that right now?"_

"The Captain adopts the "Prioritize objective over human lives" motto if I recall." Ritsuko called out, though she could feel Katsuragi's glare from the side.

" _Fine whatever, I'll go in and out. Simple!"_ Asuka called out, her EVA slowly humming back to life over the radio. " _EVA Unit-02 Dash, launch!"_

"Launch the Unit-02 Dash!" Cap. Katsuragi ordered.

" _Understood, launching Evangelion Unit-02 Dash. Deploying underwater motor and left Container No.01."_

" _Man, this new makeover is crap for my Unit's debut."_ Shinji couldn't but smile at that; definitely Asuka. No one cared more about their EVA then her. Walking towards one of the many windows, Shinji looked out in time to see Unit-02 Dash pass by him. Its left arm was a large motor like cell, pulling the EVA as it moved faster with its feet.

"It IS Asuka, so she really is alive!" Shinji smiled happily. Never did he think she's survive the Bardiel/Unit-03/Unit-04/VEELE incident. He only prayed she was still the same bother mentally and physically wise. He did not want to see Asuka with robotic parts and arms and legs like…. "Shiro…."

Shinji's eye widened as he recalled the memory of Null Unit exploding as Tenth Angel destroyed it. He felt his heart grow fast and his eye water slightly, feeling dread at the memory and thought of his brother being dead. "N-No…. No, don't think that…." He told himself, placing a hand over his eye with fear. "He can't de dead, he just can't be…."

He felt everything crash inside, but he forced himself out of that before it was worse. _If anything, Shiro would want me to help these people in any way possible_ he thought, looking up to Misato's platform. _Maybe I can…_ "Misato, what can I do to help?"

"All ships, prepare for Battle Stations 01!" the Captain ordered, the lighting in the room going red as her platform raised two large grips on either side of her.

"Roger, all ships to Battle One Stations." Makoto stated, fixing his glasses as he continued. "Shifting all control to battle command systems."

"Good; all key personnel report to the bridge. Prepare the gravity ballast."

"Roger," A technician began working on the systems, pulling and pushing certain button and levers as she continued to report. "Checking all vents."

"Focus all primary controls of the ship to anchoring plug."

"Understood, preparing the decent.

"Injector confirmed."

"Starting the timer. Preparing move for Hirnstamm Tower."

Shinji finally sighed, glaring up to Misato who seemed to think he was invisible. "You're going to make me yell huh? Didn't want to do this, but now I _have_ to yell…" he uttered, before he finally raised his voice. "Misato! Unit-01 is here right? Please, let me pilot it! I can at least assist Asuka outside!"

Cap. Katsuragi didn't reply, she simply kept to herself as usual. It should have been as clear as daylight that she had _no_ intention of letting Shinji near an EVA, but he could at least try and reason with her. He didn't notice the glares or silence from the other crew, or the girl from earlier hand tighten into a fist. "Please at least tell me you don't need me to go out there?!" he tried again; no response. At least, not to him.

"Ready the Plug-In charge."

"Roger, Plug-In charge now ready."

"Preparing entry…."

"Yes, that is correct." Ritsuko finally spoke out, looking to Shinji with barely little emotion in her eyes. "We _don't_ need you to pilot EVA."

Shinji flinched at that. Never, in all his life at NERV, fighting Angels and occasionally going crazy with drinks alongside Rei, Asuka and Shiro, all the while fighting with his father about the truth regarding his mother's death did he ever think he'd here those words.

To him it was a blessing at first glance, yet now that he heard her say that it made him feel badly uneasy. It was like he'd just got what he wanted and lost something he either wanted or needed.

 _"Separating Hirnstamm Tower."_ A voice called out, and soon the command system like control and crew were lifted off the ground. _"Command Center now being transported to bridge."_

"No… Need…." Shinji repeating, once more feeling a new sense of dread at the remark. It didn't come off as a good tone with Ritsuko, no more like a disapproving or annoyed one. "So then…. What can or… What should I do?"

"Shinji Ikari," Katsuragi stated aloud, taking off her glasses to reveal a darkly familiar emotionless glare. Shinji blinked, the dark memory of his father glaring down from above Unit-01's Cage flashing before him as Misato spoke with pure malice and hate laced in her voice. "From now on, you will _no longer do anything._ "

And with that, the command system and crew were enclosed into a sphere like piece, spinning upwards into the ceiling like that of an EVA Entry Plug. "I…." Shinji was at loss for words; he never thought Misato would be so… so… harsh.


	3. Chapter 3

**_Neon Genesis Evangelion, the End of Evangelion, and the Rebuild of Evangelion are owned by Hideaki Anno and written by Yoshiyuki Sadamoto. I own no elements from the original Manga, TV show, or Rebuild and EOE films but my OC's._**

 ** _That said, Please Enjoy The Show!_**

Talking-"Hello"  
Radio/EVA Voice- _"Hello"  
_ Thoughts- _Hello  
_ VEELE/VEELE Clones- _ **"Hello"  
**_ A.I- **"Hello"**

* * *

 **Chapter 3: Autonomous Assault Ark Wunder**

 **Command Bridge (Entry-Plug System)**

"Saturating LCL with gas mixture!"

"Charge density now cleared."

"Begin man Entry." Captain Katsuragi ordered, fixing her glasses to her collar.

"Understood." Matoko replied. In a flash the circular room the tower sat in revved to life with a multitude of flashing colors, very reminiscent to the startup sequence of an Evangelion. "LCL charge status is nominal."

"Beginning all integrated processor systems." Shigeru called out, the large screen flashing a image of a computer like screen before altering once more.

"Status?"

"All personnel are present, ma'am."

"No problems in initial contacts.

"Confirming stations." Another voice rang out along with the others."

"List 01 now cleared."

"Confirming all closure of barrier walls."

"Pressure resistance check has been complete!"

"Now increasing power generation of backup engines."

"Supplying main engine system with ignition power….."

"In about 5% it'll reach the critical point!"

"Starting up gyro compass." The older man from earlier, Koji Takao, called out.

"Stabilizers show no problems!" Hideki Tama stated.

"Commencing visual data processing…." Sumire Nagara stated, the large screen monitor flashing before it formed into a large feed of the outside. "Image is now on main monitor."

The camera feed showed several destroyers, oil construction rigs and aircraft carriers close to their ship, with several large pillars of red energy far in the distance, yet closing in steadily. "Targets are still approaching." Kitakami stated, looking from her radar to the main monitor. "They're surrounding us, Captain slow but surely."

"And Unit-02 Dash?" Katsuragi asked.

"Finished disposing its propelling arm and now switching to left hand." Makoto stated.

" _Here we go!"_ Asuka yelled through the radio link _. "Perfect…. Alright, let's do this!"_

Unit-02, through another video feed, was now directly under the main reactor. The reactor was a large oval shaped cocoon, with red linings across its blacks form connected by several large and small energy feeding tubes.

"Activating A.T Field!" As soon as the Field pulsed before Unit-02 D, the pillars of light formed large rye like pupils at their top points. More eye pilot points grew under the top ones, slowly sending out sharp points which latched on to the pillars on either sides. "Pillars are changing shapes!" Hideki reported. "And their energy is increasing rapidly!"

"They're all moving!" Kitakami blurted out, watching as the pillars moved differently than before. They now moved almost twice as fast, burning anything nearby ships in their path towards the lager vessel which housed Unit-01 and its pilot.

"Allied destroyer lost!" Shigeru reported hastily.

"Christ, it's a saturation assault!" Ritsuko realized. The pillars had seemingly formed a large dome like shielding around the large ship and smaller ones, slowly enclosing them into destruction. "It the dome hits us, its over!"

Cap. Katsuragi didn't respond, though she silently hope Asuka would be done in time before the dome could kill them. "360 seconds till contact!" Makoto yelled out.

* * *

Back with Unit-02 D, Asuka fixed her Spear of Cassius replica forward, its front blade warming up fast from the heat the powerful blowtorch like flamethrower the open center gave off. As soon as the blade was close to pure white, Unit-02 pulled the Spear back, ready to toss it forward into the reactor core. It slammed into the cover piece, the red seas under the large vessel glowing vividly.

 _This is it,_ Asuka thought to herself clutching her controls tightly. _If this works, we'll finally have this damn SEELE cruiser up and running for us! No more ocean and most certainly no more waiting….!_

* * *

"Unit-02 D has begun operations." Makoto reported, fixing his glasses. "Flowing pressure now at 300%!"

"Doesn't matter!" Ritsuko stated, looking down to the crew. "Just have all energy directed to the flywheel! That is our top priority!"

" _The 83_ _rd_ _lines ablaze! Fire Extinguishing's impossible_!" The radio screamed out. All across the fleet the many tethers which fed energy to the command ship exploded into fiery energy, letting any power they housed loose. _"The 7_ _th_ _Converter Cluster's exploded!"_

"Broken lines don't matter!" Ritsuko retorted. "Continue with the force injection!"

"Ignore all pressure gauges!" Koji ordered, fixing his console as he watched his screen carefully.

" _Now releasing locks on compressed flywheel."_ Outside atop the command ship, a large cylinder shaped object began spinning rapidly, the lighting on it pulsing at its top. Energy flowed through the hull of the command ship, with energy being forced into the reactor core. _"Energy pump for the main engine had commenced!"_

" _Backup engine operation at 80% output!"_

" _Load it up with catalysts!"_

"35 seconds left!" Kitakami reported.

"Rotational speed is increasing!" Sumire stated.

10,000 turns…. 12,000 turns….." _C'mon, just a few more!_ Koji thought silently to himself. He prayed like the others around, that would work and that they'd live. Otherwise this would all be for nothing! "Finally, Flywheel is at 102% charge!"

Critical point has exceeded!"

"We're at the final ignition phase!"

"Good." Cap. Katsuragi finally spoke up, glaring forward at the task ahead. This would take a extremely powerful amount of work, but it would hopefully pay off in the end. "Switch to flight mode."

"Roger." Sumire answered, taking the controls before her. Around her seat came up a 3D layout of all the ships around the command chip, with an orange layout of the ship statue from all 4 directions. "Now starting spatio temporal control. Switching to 3D control of vessel."

"The moment we launch, raise our A.T Field!" Katsuragi ordered.

"Rotation speed now at 36,000 turns!" Hideki stated. "All parameters now at green!"

"Contact is imminent!" Koji yelled out.

"Forget the countdown! Activate the main engine!" Katsuragi snapped.

"Roger!" He replied, pushing the large level to his side forward. Outside, the compressed Flywheel slammed down into its opening point, ending energy roaring all across the ship.

"IGNITE!" Katsuragi finally yelled out, and just in time as Asuka had her Unit-02 D slam the igniter into the reactor core. The core came to life with a powerful roaring of engine cells, creating a wave of both energy and power which destroyed the large dome in a single shot.

At the epicenter of the fleet, a large halo hovered above the epicenter of the energy release. "Obstacles now cleared!" Kitakami stated.

"Check every department!" Ritsuko ordered, the monitor around the tower covered by a white glow. "Bring all consort ships back, NOW!"

"Here we go…." Katsuragi muttered, silently hoping this would work. They'd already given their position away from the power release, this had to work! "Autonomous Assault Ark Wunder, LAUNCH!"

Outside, the command ship AAA Wunder slowly rose from the sea. The Wunder was huge compared to its many predecessors, spanning almost 2 kilometers in length with its large spiral like rib cage. The ship housed a light maroon like color scheme, blended together with yellow and light sky blue colors all across her hull.

At the front were two large front engine cells, which was before the center point that housed the command bridge underneath. Slowly the rib cage connected with its top metal layer above, with many large cannons and antenna arrays across its hull. It almost have a animal like design, with large wings and an end tail.

The engines hummed to life as the AAA Wunder rose up, light shimmering across her hull as her many escort ships hovered above the watery surface of the Arctic. Slowly the wings open their talons, spreading out like a looming vulture ready to take its prey. Under the Wunder laid a hexagonal made A.T Field, which slowly dispersed in favor of two halos which helped keep its afloat.

That is, until the hidden Mark.04-C's fired several grapples which roared high into the air. The grapple like tendrils tore right into either wing, sending blood out as they latched on tightly with an after explosion. The whole of Wunder and her crew were shaken badly by the explosion as surprise assault, clear evidence that the enemy forces weren't letting go so easily.

"Shit, mains wings have been penetrated! Damage extend is unknown!" Koji yelled out.

Katsuragi gritted her teeth, glaring at the image display of the Wunder's new injuries. "Rgh, that doesn't matter!" She grunted, gripping the railings tightly. "Prepare for fire at the targets! Flip us, take us astern"

"Solid copy, going astern! Steady the course!" Sumire acknowledged. In an instant the Wunder now faced downwards, as if searching for its enemies alone.

"Good, now drag the core blocks out of the shielding cocoon!" Katsuragi continued. Slowly the Wunder pulled itself in reverse upwards, the cocoon shield revealing itself to be larger than the fleet and Wunder's predictions.

"We have cracks appearing on the main wing beams!" Hideki yelled.

"Keep the rudder steady, bring the engines to full power! Maximize power on both ends and full speed!" The front engine cells roared to life in an instance, pulling Wunder and its targets higher. Slowly the Mark.04-C's were pulled upwards, their cocoon shield exploding apart as they were now in the air.

The Mark.04-C's were built similarly to the Mark.04, circular with red dots on their surfaces, though with center tendrils with purple and yellow colors EVA-like shoulder pylons that went around their diameter. "Core blocks are out!" Sumire screamed out.

"Hard to port, NOW!"

"Roger!" Slowly the Wunder began to spin as it point, dragging the Mk.04-C's as it did. The large vessel spun faster and faster as it pulled the target drones, slowly pulling them up to their altitude. "Thrusters now at maximum!"

"FULL BRAKE!" The Wunder immediately halted in place, the Mk.04-C's all crashing into one another.

"No sign of target activity!" Shigeru reported.

"Now, full power on main batteries! Load the energy-penetrator ammo!" Katsuragi barked out. "Connect all cannon towers to the main engine! Open all cannon circuits!"

"Roger," Hideki acknowledged, flipping through the screens as he and many others readied the cannons. Atop the Wunder, large cannon arrays came to life, their weaponry warming up to destroy their enemy targets. "Opening ammo supply circuits."

"Measurement errors being corrected in time!" Kitakami stated.

"Artillery batteries unlinked!"

"Direct aiming and manual tracking ready on all cannons!"

"We're ready then," Katsuragi stated, glaring with hatred to the target drones. "FIRE!"

Instantly the Wunder's cannons rained hell, cutting harshly into the Mk.04-C's A.T Field. The Field burst apart and the cannons loaded shell after shell into the Mk.04-C's, destroying them with an explosion of cross like endings.

"Targets eliminated!" Kitakami stated, the Wunder in turn slowly turning back to its escort ships.

"All ships, Guard State 2!" Shigeru ordered. "Prepare for Unit-02 Dash recovery!"

"Start emergency repairs on the wings with all haste!" Ritsuko ordered, signing as her hands leg the railings on her sides go.

"Jesus…" Hideki whispered, followed by anyone else who had been new on the command bridge. "We've won…."

"God, she's insane…." Koji stated, smiling as he wiped his forehead clean of sweat and look to the captain's deck. "She really is more interesting than Kaji said then…."

"So there you have it; the power go kill God." Ritsuko stated, looking to her old friend who remained silent in thought. This had been their first victory in…. Ever, really. And this time there were no betrayals, no EMP explosions, no NERV going nuclear and certainly no Unit-01 exploding…. "Wunder really is a ship of hope…."

Now there laid the other problem they'd had; Shinji Ikari, if it even was him. Then again, the other BM specimens hadn't been sent flying into far space and returned, so it was a halfway possibility that this was indeed Shinji Ikari.

* * *

Shinji meanwhile stood at her original place by the window of the Wunder's bridge, unsure of whether to throw up from all the momentum or to question what he'd just saw. The Wunder wasn't just a ship by the looks of it; no, it was like an Evangelion Something felt wrong to him, deep down. He felt like he was at NERV with the child like staff and old NERV personnel working around the clock to preform God knows what operations and such.

Except at the same time, it wasn't.

* * *

 **Quarantine Interrogation Cell 01, AAA Wunder Medical Sector**

Shinji found himself sitting in a chair, flexing his fingers as Ritsuko pulled up an image of his Evangelion. "Woah, so that's Unit-01?" he asked, surprised at how they jury-rigged his EVA into a battery. The EVA was surrounded by large nullification blocks and enclosed in the main reactor of the Wunder.

"Yes, your Unit-01 is being currently used as our main engine." Ritsuko explained, slowly pilling the feed so it showed the outside structural form of the Wunder to the Specimen. "That said, its one of the reasons it doesn't need a pilot."

"Ah…. Christ, it's huge to think that that's possible!"

"Not really; having an EVA not need a pilot was used before by the….."

"No, not the piloting bit; the Wunder! How the hell did you build something like this? The budget must have killed the UN…" Ritsuko gave a soft smile at that; the budget to build Wunder indeed an _extremely_ heavy amount to bear, but still what remained of the UN and US complied. "Still, I see your point. An EVA only used as a energy supply unit isn't really combat needed."

"Exactly." Ritsuko replied, pulling up a synchronization image of Shinji's time in Unit-01. "This, I should say, is your Deep Level Synchronization test results. Your Sync rate is 00.00%. That said, you won't be able to activate an Evangelion even if you did pilot it."

"Great…." Shinji grumbled, something he blinked in surprise at. _Am I…. Am I sad I'm not able to pilot anymore?_ He thought to himself, looking at his reflection with slight concern. _Oh God, Asuka's rubbing off on me….!_ "Oh, God I'm going to hate this…."

"What?"

"Myself…." He uttered, before shaking it off. "Um, please continue though."

"Right…. As I was saying while this is good for you, Shinji we can't overlook the face Unit-01 awakened for 12 seconds during the earlier operation." She brought up another image; this time of Unit-02 Dash atop a large metal cross, a beam of light escaping a large crack on the side. "This is where the DSS Choker comes into play."

"So that's what this thing is…." Shinji didn't like this; at least not where this conversation as going. He had a dark feeling he knew what the purpose of this Choker was, though he didn't want to believe it.

"Think of this as insurance for us," Ritsuko continued, a video feed of his Unit-01 awakening during the Tenth Angel's assault coming up next to the 3D model of the Choker. "It's our physical means to preventing EVA awakenings; as well as a symbol of punishment with our mistrust in you. You see, in the event that you fall to your emotions while piloting an Evangelion, with the risk of another Impact launching to great, the Choker will activate-"

"And kill me instantly?" Shinji finished, looking at just who would pull the trigger. _Never thought Misato could do this, but is must be for the greater good_ he thought to himself as the video faded to reveal another room beside his.

"Yes." Ritsuko answered, making the Third Child sign. He didn't like this: First NERV was him as a threat, wouldn't allow him to pilot an Evangelion's, and now had the power to kill him at the flick of a wrist. "Ugh… Woopty-fucking-doo….."

His eyes traveled from the Project E. overseer to his former surrogate mother, who stayed silently next to the side wall. "Judging by your silence it must be true…." Shinji uttered, running a hand through his face.

"You're… Taking this very well." The girl from earlier stated, looking at Shinji with slightly worry.

"Well when you've fought the universes most demonic creatures in a machine powerful enough to kill you should you fail, all the while dealing with a god awful father who has about as much emotion as a rock and trying to keep the apocalypse from happening…. You tend to lose a lot of senses and emotions…." Shinji stated, before looking more closely at the girls face. _She's looks so familiar, just who is she?!_ He thought to himself, but he didn't realize…. "Um, by the way, who are you?"

"Oh well, I guess this comes late but I'm actually Lieutenant Sakura Suzuhara, your assigned medical officer." The girl, Sakura stated with a small bow and smile.

"Suzuhara?" Shinji gave a slight bow back, before a memory flashed across his mind.

* * *

" _The hell was that for?" Shinji growled, getting back to his feet._

" _Sorry new kid, but I had to hit you." Toji stated. "Had to settle a score with you."_

" _A score? Look if this is about me setting the high record on Galaga in the arcade I'm sorry!"_

" _Yeah, it's not that." Kensuke explained to Shinji, gesturing to Toji. "It's just that his sister got hurt during the attack and yeah…. That's just him though, sorry!"_

* * *

"Wait… Suzuhara as in…. _Toji Suzuhara?_ " Sakura gave a nod, but took a step back as Shinji bowed completely. "Oh my God I am SO sorry for what happened then with the Fourth Angel! It's just I was new, and I didn't know how to pilot EVA or what I was supposed to do! And-And-!"

"Oh that? It's alright, you didn't know what to do…." Sakura waved it off with an apologetic smile, which only seemed to made Shinji feel guiltier. "Anyways, thank you for being friends with my older brother and Kensuke."

"Older brother? But you look so _older_ than him….."

"Hey! I'm not that old, I'm only 16!"

"Only 16? How do you look so young then?"

"Because it's been 15 years since the Tenth Angels assault on NERV and the Geo-Front, Baka Shinji." Shinji blinked at that, turning his head to see a familiar redhead with a cap and jacket on, though still in her previous red Plug suit.

"A-Asuka?! You're alive!" Shinji gasped, though it felt replaced by fear because of the look in Asuka's eyes and her power march towards him. Asuka didn't say a word, but she brought her fist back and slammed it forward, making a large crack where Shinji's face was behind the glass. "Yep, definitely Asuka… No one's as powerful as her….."

"It's no good. I can't stop myself…. I've holding back all these years…" she uttered, physically ignoring Shinji's comment about her.

"…. Guess you finally had reason to let it out huh?" Shinji asked hesitantly.

"Glad to see you remember I'm a lot stronger than I look…." The Ex-Second Child grunted, sighing as she pulled back her fist as she stood on the metal desk beside the wall. _This looks awfully familiar_ , Shinji thought, the memory of Asuka standing atop Unit-02 and above all else after the Seventh Angel's attack entering his head. " _That_ was from all my pent-up rage and grief.

"I… I see…." Shinji whispered, taking his seat back before he noticed something. Her eye, more specifically her left eye which was covered by a metal eyepatch. "Your…. Asuka, your left eye is…"

"Yes it is covered." Asuka stated sharply, glaring down at Shinji. "But that is none of your damn business."

Shinji gave a fast nod, quick to realize Asuka wasn't willing to speak about that personal problem. "Wait… You said it's been 14 or 15 years and yet you appear as young as the day we met…." Shinji stated. That was something that caught his attention right away: everyone aside from a few NERV personnel and the new people seemed too had not aged at all, with only small things like hair length.

"Yes…. It's the Curse of Evangelion…." Shinji raised an eyebrow at that. _The Curse of Evangelion? The hell's that, a rock band?_ He thought to himself, watching as Asuka turned and landed back onto the ground. _Wait, maybe she knows…!_ "W-Wait, Asuka! Tell me, do know where is Rei?!"

"Not a clue." Came her reply.

"No idea….? But that's impossible, I save Rei from the Tenth Angel!" Shinji cried out, feeling dread built up in his chest. _Please God don't tell me their….?!_ "W-Where's Shiro then?! You have to at least know where he is!"

"Don't know, don't care. Nevec scumbag can burn in hell for all I care. "Asuka growled, making Shinji back off slightly. _Nevec, what's what?_ He thought. _I'll have to keep that in mind, right now I have to know if-_ "Besides, so much fuss over 2 people, no one has the time to care anymore. Right, Captain Katsuragi?"

The Captain didn't reply, but the silence was enough of an answer for Asuka as she left. "Asuka!" he yelled out to, but she simply ignored him. "Damn it…. Misato, please tell me where are Rei and Shiro? Please!"

"Shinji." Captain Katsuragi stated, glancing up to him under her visor like glasses. "Rei Ayanami doesn't exist anymore."

"And Shiro Ikari is dead."

"No…." Shinji whispered, his heart exploding into blood as he heard those words. "No… No, no, no, NO! P-Please tell me you're lying! Please, Misato?! Rei can't be dead he just can't be! I…! I-I… Sh-She must be in Unit-01's Entry Plug then! Please look for her!"

"We've already conducted a thorough search inside of Unit-01 not long after Operation US." Ritsuko spoke up, a large drawer opening to reveal Shinji's previous S-DAT from before. "All we found was you and this. We've found nor problems on it, so you can have it returned to you."

Shinji slowly took the S-DAT, looking at it silently. He felt his eyes for the first time in a while water with sadness, his voice cracking as he felt back into his seat. "No…." He whispered, pulling his legs to himself. "Please, God…. Just let this be some dream….."

"Believe me Shinji," Cap Katsuragi stated, turning her head fully to the Third Child. "This is no dream: Your brother is dead, and Rei Ayanami is no more."

Shinji didn't respond, he simply pulled himself closer in silence. "Please don't leave me…." He whispered silently, a tears slowly falling down his cheeks. It felt just like before; just like that day, the day his father stole his childhood and brother away after his mother's death. "Please, big brother…. Not again…"

Shinji felt every memory his mind had of Shiro come and go fast: when they were younger, Shiro being separated from Shinji, Null Unit arriving and Shiro coming as its pilot, meeting Rei, the Sixth Angel Incident….. He felt it all collapse, all the memories and emotions he held once.

Sakura couldn't help but frown at Shinji's now emotional state; it seemed like NTI had now done a number on him. Katsuragi couldn't help but felt pity for the boy, but she easily pushed it aside. It wasn't like the specimen was the _real_ Shinji Ikari anyways, no point in feeling bad for it.

A sudden boom and she shaking of the Wunder caught everyone's attention, making Shinji look up in surprise. "W-What was that….?" He asked, rubbing his eyes from his tears.

"Katsuragi here, what is it?" Katsuragi pulled the wall phone to her ear, a grim look on her face as she listened to the situation. "Damn, so our biggest threats are here. Have all ships to Battle Station Level 01 then 10! We cannot allow the Mark.09 or that Akrid arrive to find Ikari!"

" _Ikari Shinji, where are you?"_ A voice, emotionless and cold as ever called out, and Shinji felt his heart rise faster than ever at it. The voice was…

"R-Rei? Rei, where are you?!" He cried out, standing up fully and looking around the room. Ritsuko nor Cap. Katsuragi replied to him, but the glass was replaced by a cracked metal wall. "Bitch….."

" _Ikari Shinji, where are you?"_ The voice repeated.

"I knew it, it _is_ Rei!" Shinji gasped out, looking to the side wall with shock. In an instance, Shinji slammed his hands onto the metal wall trying to get their attention once more. "It's Rei, Misato! I'm telling you it is!"

No response, aside from Sakura trying to get his attention. "Rgh…. Dammit… I've had enough….." He whispered, before raising his head with a look of determination. "REI! I'm right here!"

Not a second later did Shinji get his response, the side wall exploding with smoke and escaping air. Shinji brought his arm up, trying took look past the smoke to see…..

" _Damage on the starboard side hull!"_

" _Hull fissure on 2_ _nd_ _deck!"_

" _Pressure drop in the temporary quarantine interrogation room!"_

" _Emergency closure of barrier walls!"_

"An Evangelion?! Is that Unit-00?" Shinji gasped, looking at the large head of the EVA. It had orange-yellowish and white colors, with a large metal orb inside a metal helmet similar to Unit-00's head design. The orb spun, looking to Shinji as it enhanced its red eye.

" _Ikari Shinji, please come with me."_ the Evangelion's pilot stated, its hand opening more for Shinji.

"Don't you dare, Shinji!" The Third Child's eyes narrowed, and turned to see Katsuragi near the destroyed wall, visor half broken to show one of her glaring eyes. In her hand was the Choker's detonator, finger ready for activation. "Stay right where you are!"

"Oh, I'm so sorry Misato! I can't hear you over the bullshit lies exiting your mouth!" Shinji screamed back, glaring with newfound hatred to his surrogate mother. "Besides, could have sworn I _couldn't_ pilot anymore! Why do you still need me again?!"

"Because we can ensure your safety!" The Captain yelled back.

Shinji laughed harshly at that. "You can barely protect _yourselves_ , the hell makes you think you can protect _me_ huh?!" He asked his arm reeling up to block out an explosion which hit the sides of the Evangelion. He looked to see the ships in the far distance firing endlessly as the EVA, thought they were ineffective. "The hell are you doing, you idiots?! Stop, that's an EVA your firing at!"

"Exactly! We'll destroy all of _NERV_ and _NEVEC_ Evangelions if that's what it takes!" Katsuragi yelled back.

Shinji gasped in realization, before his glare hardened. "I knew it, this isn't a part of NERV is it?!" He asked, though he knew the answer from the get go. He felt it the moment he saw everything in disarray, the moment he didn't see the NERV logo anywhere on the ship, and most of all when he hadn't seen or heard his father or anyone else say 'Pilot the EVA.'

"Of course not! We are WILLE, a UN organization dedicated to destroying NERV and NEVEC!" Katsuragi yelled back, her grip tightening on the trigger.

"How….?! Why?! Besides, Rei's piloting that EVA!" Shinji tried to reason.

"It isn't her Shinji, I'm telling you!" Katsuragi yelled back, glaring at the Specimen with hate. "Rei and Shiro are dead!"

"LIAR!" Shinji roared back, pointing to the EVA. "If that's true, then who the hells voice is that?! The Dummy Plugs or something?!"

Katsuragi didn't reply, because she didn't have the answer to it; but it was enough of an answer for the Third Child.

"Fuck this and fuck you, Misato! You're fucking clueless!" Shinji finally growled, eyes full of rage as he rushed into the Mark.09's hand. "Screw it, I'm out of here!"

"W-Wait Shinji!" Sakura rushed forward, getting the Third's attention. She knew she couldn't' stop him, but she could at least remind him what NOT to do! "Do whatever you want, but please for the love of God DON'T pilot any more EVA's! Seriously, give it a rest!"

Shinji didn't verbally respond, but he backed more into the mark.09's hand with a nod. "I'll keep that in mind!" He finally called back, the last thing he saw being Sakura as she back off from the opening.

Slowly the Mark.09 pulled away, dragging out more metal from the interrogation room as it looked forward. Katsuragi rushed forward, watching as its head was shot before exploding completely leaving only a bleeding neck. "Don't let them escape!" She ordered, but it was too late as the metal cape of the Mark.09 solidified into a set of thruster which pushed the Mark.09 off the Wunder.

"If they've only came here for him and not Unit-01, it's possible he can still activate Evangelion!" Ritsuko yelled out, watching as Katsuragi pulled up the detonator. "Misato, quick! Activate the DSS Choker!"

Misato felt every fiber and cell in her scream to push to button; to end another BM Specimen. But her mind reminded her of the broken down look of DM-03 when he was told of Shiro's death, majorly unlike the other BM Specimens reactions before him. The detonator gave a beep, the message that the DSS Choker was too far away coming up as Misato lowered her arm.

She mentally sighed; once more she'd let her emotions slip out. "Damn it….." She whispered to herself, her eyes watering slightly at the old memories before Third Impact before she pushed those emotions aside.

Above the Wunder, Asuka sighed as she heard the orders to repairs the hull. Once more Misato had failed to activate the trigger, and once more another Specimen had fallen into NERV's hands. "I was wrong, he's now Idiot…." She muttered, glaring at the distant line of the Mark.09's thruster smoke.

"He's just a brat….." Another alarm quickly blared up and Asuka sighed. "Great, what did they send another to-?"

Then the sound came up. That twisted, evil screech, unlike anything EVA and most certainly metal on metal, roared aloud the Wunder and once more the many large cannon arrays fired all around the Wunder's perimeter. _"Blood pattern yellow detected: It's an Akrid, Category M!"_ The radio cried, and the Ex-Second Child looked to see the creature crawl on the side next to her.

She froze, her hear beating now rapidly as the creature, or Akrid, rose its head high. The Akrid's body was mantis-like, with large spiked forearms ending with a pair of finger like claws. The head was silent, before it split into sharp pointy tendril like jaws with lined spikes and teeth. Asuka felt her mind flash back to NERV, to the betrayal, and most of all…..

The Akrid slammed its arm into the metal hull, looking up then down and turning fully upside down. "This is Asuka, the Akrid is now moving towards the lower hull!" She called out, rushing back down the opening. "Mari, it's heading for Unit-01! Shoot it down!"

"I'm on it!" The Fourth Child's Unit-08 rushed back, head looking around all areas of the Wunder's hull as the Akrid screeched once more. The sight of Unit-08 sickened its mind as it crawled now towards the pink EVA, mouth splitting open once more. "Oh crap, here he comes!"

The Akrid and Unit-8 ran faster, metal screeching as they grew closer and closer. The pair finally collided, Unit-08's feet screeching as Mari attempted to halt the Chryatis Akrid. The Akrid clawed and punctured into the arms, Mari gasping as the monster snapped its alien jaws. The tendrils dug into the shoulder pylon, tugging into the armor and the Progressive Knife.

Mari finally gasped out in pain as the Akrid clawed its other arm into the second arm, slamming its legs into the chest, tugging the chest plates as it pulled its head up and tried to snap Unit-08's head. "Crap, I'm falling apart!" Mari cried, finally screaming as the Akrid finally grabbed onto the head of the EVA; the metal giving way to the powerful demon. "Ahhhhh!"

" _All cannons open fire!"_ Captain Katsuragi's voice ordered, and in an instant the cannon arrays roared to life once more. Explosions rattled the WILLE Evangelion, sending the older Fourth Child shaking around her Entry Plug _. "Unit-08, hold off the Cat-M Akrid until we can target the Akrid's TE supply sacks."_

"Not as easy as it looks, Captain!" Mari yelled back, gasping as she felt something burning across her head and neck. She looked to see the Akrid's jaw letting out an orange/yellowish liquid out, spilling like acid onto Unit-8's head and onto the neck. "Asuka, whenever you want to come out and play I'd really love it!"

Unit-8's shoulder pylon and blade finally broke apart before the sound of flying bullets flew through the air. The noises burned cruelly and fast into Unit-08 and the Akrid; the explosion killing the Akrid in a powerful blaze. The Chryatis Akrid screamed in agony, both bubbling before it exploded into Thermal Energy. Unit-08 tilted, finally sliding down next to the Wunder hull. "This…. This is Unit-08, I…." Mari gasped in air, gripping her shoulder as her glasses dropped slightly. "The Cat-M has been dealt with…."

"….….." Mari and Asuka, finally arriving in Unit-02 D, Gatling gun letting hot steam loose from its barrels, stared down the burning carcass of Thermal Energy. This had been the first time a Cat-M had attacked _them_ on their own battlefield, even without Thermal Energy being used. It was either just here as a scout to find or get BM 03 for God knows what reason….

….Or even worse, a dark omen for a more crueler coming.


	4. Chapter 4

_**Neon Genesis Evangelion, the End of Evangelion, and the Rebuild of Evangelion are owned by Hideaki Anno and written by Yoshiyuki Sadamoto. I own no elements from the original Manga, TV show, or Rebuild and EOE films but my OC's.**_

 _ **That said, Please Enjoy The Show!**_

Talking-"Hello"  
Radio/EVA Voice-" _Hello_ "  
Thoughts- _Hello_  
VEELE/VEELE Clones-" _ **Hello**_ "  
A.I-" **Hello** "

* * *

 **Chapter 4: New NERV**

" _Shinji….. I know you're here…. Just hold out for me…."_

Shinji gasped as his eyes snapped wide open at the voice, the sunlight meeting his gaze automatically. It'd felt so real, so close and very much familiar. He squinted, running his eyes with a groan, pushing the thought aside for the time being. He slowly pushed himself up; Shinji looked across the room, gaze meeting the long figure in the room. "Rei!" He cried in revelation, eyes shimmering with hope. _I did it_ , he thought to himself. "I really did saw you!"

His nostrils let out air sharply, eyes narrowing with a clenched fist. "Misato, you lie….." he growled softly, too asleep to scream or snap with rage. He felt more hate burn awake, before finally throwing the covers off. Once more he found himself in- "My old clothes?"

His clothes remained the same as before his 'assimilation' with Unit-01: a white button up short sleeved shirt with a breast pocket, a grey short sleeve T-shirt underneath, along with his casual black jeans and white sneaker shoes.

Rei did not speak, nor move or show any emotion as almost eerily how she did when Shinji first met her. She simply blinked, speaking emotionless as ever. "Please, this way." She asked, or rather stated, to the Third Child. Shinji watched her face for a moment; somewhat looking for anything that seemed different.

Nothing.

He found simply emptiness in her eyes once more. _This is…. Strange_ , he thought silently as he nodded to her. _Rei started to show emotions before Unit-01 was 'awakened,' whatever that means... Is this a front; some sick act to hide herself from the Commander? Wait… Is Gendo even alive at this point?_

The pair found themselves traversing down an angled elevator shaft, their elevator only holding a dim light for them to see one another. Shinji kept quiet, but dope down he'd wanted to hug Rei and cry his eyes out knowing she was alive.

But if this really was a false persona she'd put up, an act to fool Gendo he realized Rei couldn't show emotion either _. Maybe I should try the same act, you know? Try and have one front the confused boy when in actuality I'm searching for answers._ He thought to himself, finally speaking up. "U-Um, Rei I…. I'm really glad to see-" Shinji was cut off when the shaft ended with a blinding flash. He found himself now staring as a ginormous inverted upside down pyramid of stairs. "Oh my God…"

He could see _clouds,_ literal white clouds, in the Geo-front, or what he assumed was still the Geo-Front. He looked from side to side, finally noticing the skyline of cratered concrete which met the blue sky daylight. "Wait….. I thought the Geo-Front was enclosed underneath Tokyo-3, why is the Geo-Front so exposed?" He murmured, his fixed look exploring lower to NERV HQ.

Or better yet, what _remained_ of it.

The once lush green landscape was now as white, dark and rough as the moon surface he'd seen hundreds of times: riddled with large and small crater holes and giant splats of blood. The once large diamond shaped hole was now filled be either blood or liquid Bakelite. The familiar smooth and flat NERV pyramid now seemed obliterated, a red pool of blood or Bakelite at the lower side with the far tall building stuck close towards the inverted stair pyramid like wall.

"Dear God, is that NERV Headquarters?" he gasped in horror; so much for the acting idea. Never had he thought things would escalate to this sort of grotesque crisis; it was like some sort of battle, or sad last stand confrontation. "What…. What happened?"

The pair finally exited their elevator and passed by many horrifyingly familiar places: the old door which now sported a bullet riddled NERV logo, the escalator Shinji was slapped at by Rei now bleak and light less, the old EVA and cargo train hub now blocked off by Bakelite with light openings from above, and finally Unit-01's EVA Cage.

Shinji felt his mind revved to life with memory; Gendo ordering Shinji to pilot after years of neither seeing the other, Misato giving orders from Central Dogma, then Unit-01 ripping out of the Cage and forcing an Entry Plug into its back opening for Shinji to fight Zeruel came to his mind. The whole Cage was exposed now to the sky, completely darkened with rust and an almost dark maroon glow to it. He could even see the old observation platform roofing above Unit-01's Cage ripped open, rusted and still giving away slowly to time.

"It really has been 14 years…." He uttered, watching the clouds slowly pass before he heard it. He thought it was Rei, but no it wasn't; it sounded calm, peaceful, with a melody added in. It was a…. "A piano?"

Shinji's eyes widened only more to the melody: it was Ode to Joy, or at least had a familiar peace to that of it. He walked, careful of his steps to see a reconstructed floor at the bottom of the previous LCL pool. He saw in the center of the bottom floor a live green tree, a piano, and a person.

"Who is….?" Or rather, a teenager. Shinji blinked as he saw the piano keys moving with a collect trump of music, his white and silver like hair waving in the slow wind as the teen aimed his face upwards. What was odd though, was his attire; it was exactly like Shinji's. And his eyes opened; deep crimson close to maroon with a look of happiness and pleasure. _Okay that's not creepy at all,_ Shinji thought silently.

Shinji blinked, he hadn't thought this person would notice him. He stepped back quickly, looking back to see Rei motion towards another elevator. He nodded, silently following her.

* * *

 **Undisclosed location, NERV Headquarters**

"What is this place?" Shinji found himself standing before a large pod like object. The pod was designed similar like that of the Wunder reactor WILLE had Unit-01 encased into, with wires large and small attached to its sides, and only a number label to help give difference. "Is that….13…?"

"Yes." Shinji looked up to see an open platform before and above him, a familiar character standing atop. He still wore a black long sleeve with a gold lining at the zipper, a dark maroon shirt noticeable underneath with a red and black visor across his eyes. He also sported dark brown hair, with a newly found beard as well. "It has been a _long_ while, hasn't it Shinji?"

"Gendo Rokobungi…." Shinji murmured aloud, blinking at the sight. He was surprised to see his father still alive, even with no one else in the base. Now that he thought more about it, it seemed that NERV Headquarters was completely abandoned save for Rei, the other child, Gendo and himself. "Yeah, it has been a while…. Tell me, what new contraption have you cooked up huh?"

"Evangelion Unit-13, for you and the second pilot." Commander Ikari replied calmly, ignoring his sons question as another light coming up opposite of Rei. Shinji looked to see the white/silver haired albino boy standing in the spotlight, smiling softly to the Third Child.

"It's you, the pianist from earlier!" Shinji cried out in realization. He hadn't thought of it, but now he could see the lines forming. Gendo Ikari, the second pilot, Rei and the Evangelion pod….. "You want me to pilot again don't you…?"

"Yes. When the time comes, you will pilot the EVA along with him." Gendo stated, turning around to make his leave. "That is all."

"Wait, Gen…. Commander!" Shinji called, causing Gendo to pause for a moment. "I still have questions I want answered and things I need to know! What happened to NERV? Why's WILLE attacking your Evangelion? What is NEVEC? Where's Shiro?! Gendo!"

Gendo didn't bother replying, time was of essence to him and SEELE's plan and he wished not to waste any more time as of now. He simply looked away, turning back forward to proceed onto to do God knows what. Shinji watched Gendo finally leave, making him sigh with irritancy. _Once more,_ He thought annoyingly. _I'll have to get the answers myself. Hopefully they haven't locked down the MAGI system to much or anything._ Shinji finally fixed his hair back, making his leave as the second pilots spotlight went off, along with his silhouette.

"Time to go," he murmured, making his leave.

* * *

 **2nd Central Dogma Command Center, New NERV Headquarters**

Since then, Shinji had tried getting into the old Command Center, hoping to find something from the old machinery at the bridge like the MAGI or a computer terminal, though it seemed all exits, entrances and openings done by the 10th Angel were sealed off. He assumed this was mostly done after the 10th Angel incident, as Central Dogma was ripped apart for the most. It took a while of so, a few hours really, but he finally found another chamber of interest: another replica Central Dogma.

This one, unlike many other rooms was actually well and lite up. He found the Command Center was darkly and dusty though from the many forgotten years of its operational statue yes, but still he'd found his objective: one of the three MAGI Super-Computers, Melchior.

The old NERV security system was a haywire of a mess as the computer was still logged onto even after so many years by one NERV technician, though it was seemingly ripped apart and stitched back together with old files scattered and many weak firewalls collapsing with the push of a few buttons. From what he recovered before Rei had was told to show his current 'room,' Shinji managed to find a few key moments in the NTI Aftermath Files:

 **UN Anti-NERV WILLE EVA Force established in 2019**

 **Unidentified creature's code named 'Akrid' epidemic in 2018**

 **Anti-Akrid/ NERV New Evangelion Vital Efficiency Commando-Force (NEVEC) established in 2020**

 **NERV Headquarters assaulted in 2022**

Shinji felt dread built up at the last one, that and the Akrid title. Whatever this Akrid was is must have been a serious threat, as NERV wasn't one to see small and large terrorist activities or rip-off EVA products as extreme threats with the previous Angel assault.

Now he was in a single bedroom, empty save for a clean bed and sheets, a phone box that didn't have buttons to dial with, and a side compartment he assumed would be where he got all the necessities such as food and water and clothes from, topped off with a small table.

"Guess they don't want me calling for help." He whispered, tugging his collar slightly. The wall compartment snapped open, and out came a tray with…. "Can't even make food, huh old man?"

Shinji sat back onto his bed, tray on his lap. _Can I even call this food?_ He asked himself mentally with a concerned raised eyebrow, looking at the tray with liquid like food. He knew NERV was in shambles yes, but he didn't think it was to the point where food was scarce and in rations like this! "Well, I'm probably not going to be allowed to the kitchen for the time being, so might as well try…."

A few minutes later and Shinji found himself wandering aimlessly around NERV HQ. He pondered when he was in the room, not even bothering to realize the damn door was unlocked for him. _I'm so fucking naïve sometimes…._ He thought to himself, taking careful steps lower into NERV. Need to find Rei, hopefully she can explain what happened after so long.

He found himself in another rebuilt section of NERV, the logo now designed more pixelated on the metal flooring. "Rei!" His voice echoed with his silent footsteps, eyes searching for the blue albino girl. He passed through, what he believed to be was, a bicycle station, several vending machines and more wreckage. "Rei, where are you? Rei!"

It was an honestly terrifying feeling to Shinji; walking through what only be viewed as an EVA weapons vault felt like a unrespected grave site more so than a vault, there were so many giant guns laid everywhere he wouldn't be surprised to see destroyed EVA's there too. The many times he found wreckage were disappointingly familiar places to him, which only pained him inside more. Worst part was the silence that welcomed like an open grave, the only sounds of whirling automated tracks moving many machines through the inner highway like system of NERV making him feel so small in comparison.

"What the hell is all of this….?" Shinji murmured, looking forward at the giant complex before him. He passed through several rooms and such, finally finding a stair way that led here. The complex room had a large circular opening, the center housing several pillars in a hexagon patter with large platforms and strange symbols on them. In the center was a bulkier metal pillar, glowing red wires connecting to some sort of device at the bottom flooring.

He looked around the ginormous chamber and outline of the center machine, looking for any signs of Rei. "Rei!" He gasped, looking to see a small room size shack next to the machines circular outline. Shinji wasted no time in heading down, moving with quick pace to get to his friend-

Shinji stopped, letting his mind work just outside Rei's 'home.' Ever since he and Shiro met Rei, the two had gotten much closer together now that he thought of it more, going so far to physical contact like hugging during that last moment with Unit-01. It didn't feel like they were in the friendship category anymore though, no it felt more like…..

"N-No, not now…" The Third Child uttered, shaking his head with a tiny blush. "Can't get distracted; just go in, talk to Rei, and go back to your room Shinji. Simple…! Yeah, like I haven't heard or said that before…."


	5. Chapter 5

_**Neon Genesis Evangelion, the End of Evangelion, and the Rebuild of Evangelion are owned by Hideaki Anno and written by Yoshiyuki Sadamoto. I own no elements from the original Manga, TV show, or Rebuild and EOE films but my OC's.**_

 _ **That said, Please Enjoy The Show!**_

Talking-"Hello"  
Radio/EVA Voice-" _Hello_ "  
Thoughts- _Hello_  
VEELE/VEELE Clones-" _ **Hello**_ "  
A.I-" **Hello** "

* * *

 **Chapter 5: New Faces**

 **Ayanami Rei LCL Facility, New NERV Headquarters**

"Uh, Rei? Are you there?" Shinji walked forward, pulling the shower curtain that was Rei's wall to the side to see her….

Naked.

 _Again_.

 _Oh yeah, definitely past the friendship category…._ He thought to himself, turning around with a mad blush. "J-Jesus, Rei! Don't you remember last time?! Put some clothes one!" he cried out, unaware of the emotionless look the First Child gave back.

"Only if I am ordered to." Was her reply before the sound of a plug suit activating told Shinji he was in the clear to look once more. He turned back to see Rei, this time completely clothed in her black plug suit and A-10 Connectors, standing with a stoic look.

Shinji felt his chest tighten all of a sudden; this felt oddly familiar, and not in the good or funny way anymore. The look he found in Rei's eyes was the exact same as their first encounter after the 4th Angel; dead and stoic. He took a step forward, looking down to see a sleeping bag which he assumed was hers and stepped back.

"U-Um, hi…. Rei, I wanted to come and say thank you." He explained, reaching into his back pocket to pull out his S-DAT. "I wanted to thank you when we first arrived but I didn't want to mess anything you were doing up or something like that…."

Rei stared at him calm and silent, making him falter slightly. _If this is an act, Rei you sure as hell know how to play it off._ He thought before speaking up once more. _Alright, I got to try and make conversation; maybe key words or something, or sign language, hell anything to know what happened!_ "I uh saw you got a new plug suit?" He started up, giving her a smile as he noticed it more. The plug suit was for the most part the same only now jet black with small red, green and gray areas on the arms and legs. "It-It looks good on you- I-I mean great on you! Yeah, great! I just…. I'll have to get used to seeing you in black."

 _What the hell's wrong with me right now?!_ He thought with worry. _I never acted this way with Rei, not like some sad sick boy in love! It has to be a coincidence, probably just some distortion crap from leaving Unit-01 nothing more nothing less!_ Shinji felt his mind go back to what he was thinking earlier, and he froze up on the inside. _No…. No, no, no don't tell me…. I…. I'm in…. I li….. I…. what the hell….?_

Rei simply stared at him, either in uninterested or silent conversion as Shinji looked back to her. He found neither, just her red eyes watching with detached gaze. "I uh…. I noticed NERV HQ looks a lot more….. Open, doesn't it?" He asked, trying to raise an answer with a change in subject, but only getting silence as an answer. He finally sighed, the thought of giving up quickly passing through his mins as he started going into all the bottle up questions. "Look I'm just going to be realistic about this uh… Do you know why Misa… _Captain Katsuragi_ is going up against NERV and not the Angels?"

"…"

"Do you know what Father is doing here?"

"….."

"What happened to everyone after the 10th Angel attack….?"

"…."

"Please tell me Rei," Shinji looked fully into Rei's eyes, concern and fear rising in his voice as he spoke. "Do you know anything about where Shiro is or anything at all about what happened?"

Shinji noticed Rei's eyes adjust open barely by a millimeter, before he finally got a response. "No, I do not know." She stated, calm and passionless as before.

"I… I see…" Shinji murmured, frowning slightly as the answer. "No surprise there, I suppose, with Father more than likely moving to keep anything about the previous incidents locked….."

"By the way…" he continued, looking up in more confusion. "When did you wake up from Unit-01?"

Rei simply blinked in confusion, much to Shinji's dismay. _Don't tell me she's amnesiac?_ He thought with fear, saddened at how she could have lost her memories of the past. He sighed for what felt like the millionth time, looking up to the far ceiling above the rooms open roofing. "This isn't even a _real_ room…" He felt memories fly into his head; finding Rei's room completely dirty and unhealthy with Shiro. "It is familiar, you know? Seeing you in a room similar to this, but still…."

 _Even then you had a room_ , he continued in thought. _You had a real bed, more clothes, real food and letters and dished and a shower and a window to see the world through and books…_ "What, pray tell Rei do you normally do to pass the time?"

"I await for orders." Came the answer.

"You…. Don't have any books here…." Shinji murmured, the image of Rei reading one of her English books blossoming in his head. "Do you read at all?"

"Read...? Would Rei Ayanami do that?"

"Yeah, don't you remember? You used to read a lot!" Shinji exclaimed, smiling at the blue albino who stared in slight concern. "You used to have books in your room, then…."

"I see."

"I have an idea!" Shinji finally exclaimed, smacking his fist into his other hand. "I'll head to the library and get some for you!"

"If I remember correctly, you used to have an English book with you all the time, so I figure that's what you enjoyed reading." Shinji explained, already as to where the hell the library was.

"Like?"

"Yeah, at least I think so!" Shinji replied with a friendly smile.

Rei's eyes gazed into his brown, a hint of slight interest in them. "And what does it mean? To "like?"

"To like?" Shinji asked, before giving her a somewhat reassuring smile. "To like is to…. Well… It's sort of like a love for something, a passion if you will. You find yourself attached to whatever it may be; an object, a person, a building, a city, an even a planet or the whole of the universe. And the more you're attached to it, the more you find the desire to enjoy it, or at least that's how I view liking something… Anyways, I'm going to get those books for you. See you in a bit!"

"…" Rei stood there in silence as Shinji left her, processing his words. To 'like' was to find interest and, if possible, love in something physically or mentally. Was this something the Rei _before_ her possessed? Or was this something completely new to her ancestors and descendant clones? "Am I…. Defective?"

* * *

 **Undisclosed room**

NERV Commander Gendo Ikari and his companion Sub-Commander Professor Kozo Fuyutsuki stood below several hovering objects. The objects were all the exact same in design; once back monoliths with a triangular symbol with a snake wrapped around an apple with the German word "SEELE" and a number on the front.

The seven objects glowed with a red mist on the screen like front, digital linings moving vertical on the monoliths. "So SEELE continues to be silent?" Prof. Fuyutsuki noted. Ever since the NTI, the Council of SEELE was destroyed on the physical plains they sat on, later fully reformed into the NERV database as Artificial intelligence systems forever watching Ikari's actions. They weren't the original Council led by Keels son rather Lorenzo himself, yet they still monitored Gendo with little to no concern or effort, always to make sure he'd stay on track for them. "Do they still move to maintain this?"

"Yes, there is no need for them to speak." Gendo replied, his visor reflecting the image of SEELE 01, Lorenzo Keel hovering before him. "The Human Instrumentality Project and Human Recalibration Venture shall be fulfilled as promised by the Dead Sea Scrolls and their secondary scenario."

"Then pray tell Ikari, do you plan to use….Unit-13 for the next mission this time?" Fuyutsuki asked with concern. Ever since the Evangelion's birth cycle, the years it's been in suspension and calibration have been for nullifying its soul, for better or worse. He feared it would be similar to _then_ , only this time with the power of a God at _his_ side….

Gendo didn't respond, but it was all the professor needed from his younger companion. "Very well, though I shall watch on the side lines with your plans." Fuyutsuki stated, looking up with a slight glare to the monoliths of SEELE. "For Yui's sake, at least."

 _And for your older and younger son's sakes_ , he finished to himself.

* * *

 **Unit-01 Previous Cage, New NERV HQ**

Shinji hummed softly to himself, pondering on just what had occurred so far. So far he'd been viewed as someone easily weaponized when in control of an EVA, and now here he was being told _not_ to pilot EVA again. For the most part, he couldn't understand just what the hell was going on or happened in the previous years of his vanishing, or sleep or whatever coma like state he was in with Unit-01 and Rei, so he was now thinking to himself.

For the most he was able to make out that Unit-01's awakening (as Ritsuko has called) created some sort of rift in NERV tech and NERV command. The rift grew bigger and this probably made WILLE and this NEVEC force he hadn't seen as of yet.

And then there was the Akrid detail and NERV assault incident which had stayed out in the air at the moment. He assumed NERV was assaulted after the Akrid incident, and that's where the rest was blurred in classified or lost information.

Then there was the problem with Rei and Shiro, as well as why everyone who was Ex-NERV saw him like he was some bad omen. Had he done something unknowingly during the 10th Angel's attack? Or did NERV go and do something drastic as always and blame Shinji for it?

Shinji finally let loose a sign, rubbing his temples. "I need pencil and paper if I'm going to figure all this crap out…." He uttered to himself, laying back and looking to the sky. He blinked, smiling at the familiar sight of the clouds. "At least the sky isn't read or black or some shit like that…."

He shut his eyes in stress, breathing silently as the clouds rolled by. The he heard it; the piano. It was so soft and sweet, like a reassuring voice calling out to him trying to assure him everything was fine. And for a moment, he felt like it worked. He heard their strings and keys continuously echo in the large abandoned cage, followed by silence. And a voice. "Come down here, Shinji! Let's talk." The voice, young and male with a tone of fervor called out to the Third.

* * *

 **Pianist's stage, Old Unit-01 Cage**

Shinji found himself sitting before a beautifully polished Yamaha piano, which glistened sunlight off its black framing as the pianist who'd spoken up before watched with interest and a friendly smile. Shinji moved his hand to touch the piano, before pulling it back and turning to the pianist with confusion. "So um, when did you want to talk or….?" He trailed off, looking into the boys crimson eyes.

"I heard musical duets can be dialogues." The boy replied softly, gesturing to the large instrument. "Give it try, why don't you?"

Shinji calmly looked back to the piano, unsure of what to do. He'd hear of several piano songs before yes, but he didn't really understand the basics, nor where or what to accomplish. "L-Look, I don't want to come off as rude or anything but I'll pass." Shinji vocalized, frowning slightly at the discomfort he now felt. In a sense he felt cornered into trying the piano, and yet he was still open to do as he wished.

"You know it's important to try and change with new things to live on, right?" the white albino questioned softly, walking over casually beside Shinji. As he did, Shinji felt his heart rocket slightly up either from embarrassment of being so close or…. _Who the hell is this guy? He feels so… nice and friendly to be around all of a sudden,_ he thought abruptly. _That's odd, usually everyone I'm around nowadays has some angry or annoyed or emotionless aura, but not him, and he gives off a heart-warming and gentle one…. Strange._ "Here, try this."

The boy played several keys in simple melody, before gently taking up Shinji's hand. "Look here, all you have to do is press the keys right around here." He explained, placing Shinji's hand above the keys. Shinji gulped, now feeling a sense of nervousness before he gently pressed down on all keys. The melody was replaced by a jumbled sound and the Third quickly pulled his fingers up, looking to his pilot ally who had a smile in turn. "Try again, just press the keys one at a time."

"One at a time…." Shinji repeated, and ever so gracefully he did so. The keys played the earlier melody separated somewhat, before Shinji attempted it with slightly faster speed. Shinji gasped in surprise; there it was. The melody, he'd played it! He smiled somewhat at this, almost like a child learning a new word. "Hey I got it!"

"See, what did I tell you?" The albino haired boy smiled at his friend, gently pushing him to the side as he sat next to Shinji. The pianist played another theme, this one slightly faster as he used both hands and spoke, "Here, try that one."

Shinji gave a small nod, gently pressing the keys as he did it twice, finally accomplishing it full with a secret third attempt. The two then stared at each other in the calm wind, as if in a silent conversation or congratulation to Shinji before the albino boy raised both hands. With almost lightning fast speeds, the pianist's fingers stroked and hit keys faster than Shinji could blink.

Shinji blinked, before he realized what the pianist had done; he'd set them both up to play this! He smirked, almost cockily as he quickly replied with playing the keys from before. "Yes, yes just like that!" The pianist encouraged with a happy smile. "We sound perfect, you and I!"

And just like that the pair played their song of joy, one that brought peace to the young Shinji more than ever before. For once in a long time he felt like he was a true peace; not stressed, not pilot, not even dealing with his old roommates or the loneliness that almost took him so long ago.

No, he felt true, calm, real peace.

The pianist gave a small laugh of pleasure as they stopped slowly playing, taking in the calm air with a happy tone. "Music truly is fun! It's really amazing what a pair of people like us just now can achieve." He stated.

Shinji smiled at that. "Yeah, it really is huh?"

The pair played slightly more for a while, cracking small jokes as the sun slowly passed by. "Thanks again for the piano duet we did." Shinji credited his newfound friend, gently smiling to him. "I haven't had this much fun since I was merely 6 or 7!"

"Me too, we should try this again." The albino boy encouraged with a smile, fixing his hands into his pockets. "By means stop by anytime down here, Shinji Ikari. I'd love to play again with you sometime soon."

"Of course!" Shinji replied, before he realized something important. All this time the pianist had known his name, and yet he never gave his own. "If it's alright with me asking, what's your name?"

"Oh me? I am Kaworu Nagisa, NERV's previous Fifth Child." The albino haired boy, or Kaworu as he'd stated, spoke with ease and another warming smile to his friend. "And like you, dearest Shinji, I am a child bound by fate….."

 _ **A/N: Now we're getting into the meat and greet of it all: Shinji meeting Kaworu, old man Gendo, and Rei! But don't worry dearest readers I'm not going to butcher the story to the point where you question what weird is how 3.3 did or leave you praying I finish the rest of this story. I will be trying to upload still once a weekends, maybe push to upload 2 chapters per weekend but only time and school crap will tell.**_

 _ **That said, this is the KnightOfZ3R0 signing off!**_


	6. Chapter 6

_**Neon Genesis Evangelion, the End of Evangelion, and the Rebuild of Evangelion are owned by Hideaki Anno and written by Yoshiyuki Sadamoto. I own no elements from the original Manga, TV show, or Rebuild and EOE films but my OC's.**_

 _ **That said, Please Enjoy The Show!**_

Talking-"Hello"  
Radio/EVA Voice-" _Hello_ "  
Thoughts- _Hello_  
VEELE/VEELE Clones-" _ **Hello**_ "  
A.I-" **Hello** "

* * *

 **Chapter 6: The Truth and All It Implies**

" _Shinji….. I know you're here… I swear I'll find and save you….. For Rei and…."_ A pair of lone blue eyes pulsed in the dark with a robotic like growl which echoed across the abyss of dark. _"For mother…"_ Shinji awoke with a gasp as he clutched his bed sheets tightly. His eyes darted left to right with fear, looking for the origin of the voice. He found nothing, only himself and his empty room with his broken S-DAT. The Third Child sighed, falling back onto the bed. "It's that voice again, the one I heard back on the Wille ship and when I showed up…." He murmured to himself, pulling his eyes up to stare at the ceiling. "It sounds so damn familiar… Just who is that….?" Old Unit-01 Cage, New NERV Headquarters

"Oh, good morning Shinji!" Kaworu was honestly surprise to see the Third Child at his piano stage so much earlier than he, yet it brought him joy to see his new friend look to him with happiness; true happiness. "Your here rather early."

"Yeah I don't have much too right now as Nerv TV isn't exactly working." The Third joked, getting a slight raise out of himself as the Fifth before the duo hit it again with the piano. Shinji felt relief come up once again, the feel and gentle caressing of the piano gave such a soothing vibe that made his hear beat ever so calmly.

He pondered for a moment as to why Rei hadn't looked into reading the books he'd brought her, only barely so touching one of them. It must have been because of her absence, or maybe something entirely different? He simply shrugged it off, humming to the sound of the piano.

A few hours had passed since then, and the pair found themselves staring up into the starry night. "So you like looking above to the stars?" Kaworu asked softly, gazing up into the dark and bright night.

"Yeah, it always kept me going in a sense you know? Motivating me to go far just like Shiro encouraged me back then…." Shinji trailed, frowning at the memory of Misato and Asuka's words.

"Oh? Who is Shiro?"

"Shiro is my older brother, he used to pilot EVA too just like me and a few others!" Shinji explained, smiling at the distant memory of himself and Shiro laughing or conversing with true emotions and strong family bonds. "He used to always tell me that I meant the world to him, and I always believed him. He put his life at risk always for the greater good and my safety, so in a sense he was the perfect brother…."

"You would have like him," he continued, not noticing Kaworu watching him with interest and a small grin. "He tried to always make jokes and make light of dire situations, and we always tried to raise a smile out of someone, probably everyone…. Yeah, he was great, still is…."

Kaworu took in the words calmly, staring up with newfound interest. He'd never knew of a Shiro Ikari up till now, though he'd heard of there being a rogue Evangelion Unit-Null which had moved to support NERV Headquarters during the Angel War. _Hm, I wonder if he is another like myself and the Ayanami girl._ He thought to himself. _Perhaps he is the later on after my dissension or ascension… Or perhaps one like that of…._ Him _….._

* * *

 **The next day**

"Here you are." Kaworu held out Shinji's S-DAT, headphones wrapped softly around its casing. Earlier Shinji has asked if Kaworu could repair it, to which the boy replied with acknowledgement. It had taken an hour or so but the Fifth was easily able to repurpose the device to its original function; to play simple music. And to Kaworu's surprise, he'd found Shinji's music quite nice, the songs acted as sorts of emotions the young Third had collected and still held onto. "It should play perfectly now."

"Thanks Kaworu! Man, you are the best you know?" Shinji thanked his friend, placing his S-DAT into his back pocket. "I swear you could do anything with the knowledge you possess!"

"Oh it's nothing, just knowledge I've picked up in my years of being on this world." Kaworu blushed slightly at the recognition of his knowledge, happy to see his friend smiling. But something felt off in his smile; it seemed almost deterred and saddened by another situation. "You seem somewhat deterred by something; what's the matter?"

"Well…" Shinji sighed somewhat feeling pang as his emotions spiraled indifferently once more. "I'm just thinking out my old friends…."

"Your old friends?" Kaworu inquired.

"Yeah, you see there used to be a city above NERV HQ and the Geo-Front, uh Tokyo-03 as it was labeled." Shinji explained, looking up and almost half expecting to see the ceiling city there at the dome top. "A lot of people used to live there: me, Shiro, Misato, Asuka, Rei, Toji and Kensuke, my classmates… I didn't know it but I was honestly asleep in Unit-01 for close to 15 years and since then…. Everything's changed since then, you know!"

To be honest, Shinji hadn't recalled his friends until earlier when he was given a spare white shirt to wear. The problem was, it was someone else' button up shirt; someone he knew especially. It hurt him to see that is was one of his old friends rather than a new one, which led him to fear the possible inevitable.

"And those changes scare you as they are too much for you to handle; you're in pain." Kaworu recognized, his smile no longer across and replaced with a somewhat emotionless look. Yet his eyes held a firm grip on a small spark of anger to the past and the Lilim that hurt his dear friend than…. To treat the Lilim Catalyst User this way as it was now, even if he was one of _them_ , if felt so inhuman and cruel… so wrong!

"Yes, I…. I'm just so worried about them, Tokyo-03's people, everyone who was here then and…. And…." Shinji felt his eyes water slightly, before he finally cried out in fear. "The knowledge of not knowing and the fear it brings me it…. I don't know, it-it scares me so goddamn much!"

Shinji, for the first time since he was merely a child, felt so helpless. He'd always promised himself never to revert back that way, to the crying child who was too pathetic to realize what happened before him after their mother's death and to stay strong for his friends and family…. And yet now that persona was slowly coming back up, pushing away his once teenage and mature like behavior in favor of this one as the whole world was completely different now!

Kaworu didn't respond, yet his eyes and facial expression showed one or remorse and dread; as if fearing for such a moment like this. He frowned and stood up, looking to Shinji who turned with hidden fear. "Do you wish to know?" He asked, internally dreading Shinji's nod more and more.

* * *

 **Geo-Front outer layers**

Shinji clutched the chain tightly, yet head feared it would fall off before himself. He'd taken as bio-suit as per Kaworu's instructions as his body wasn't used to the toxins that apparently filled the air outside the Geo-Front. He walked somewhat quickly, moving to stay behind Kaworu as the Fifth walked of so casually. And they arrived at an apparent observation platform. "Here we are," Kaworu stated, glaring forward as Shinji regained his breath. "There will be a break in the clouds; there you will see your answer…."

The dark clouds quickly rolled past or through them, giving way to reveal to Shinji just what the world truly looked like now. "Oh my god…." He gasped in horror, eyes widening more and more than ever. "What is this….?"

The once far moon was now closer to the Earth or vise-versa, with large red linings forming square patterns with noticeable ginormous blood splatters and clouds across its fast spinning dull grey form. It sat there, alien to Shinji for the first time, which only helped build up dread and fear as he looked to the surface.

Or rather, looked _down_ to it.

No longer was NERV Headquarters in the ground-no, Shinji was they were seemingly high in the air with a single metal shaft like pipe that connected the smoothed out inverted pyramid to the cracked apart, blood red surface. Hundreds of Angel energy crosses hung in the air like twisted omens or reminders of the surface horror, with what could only be described the side of a giant red jaw opened on the surface with thousands of explosion craters all across and around it. In the craters he could barely make out puddles or blood or orange glowing liquid, with small inhuman cries or roars echoing all around.

"This is the real result of your ascension with EVA Unit-01, the aftermath of Third Impact." Kaworu described, looking forward with hidden guilt.

"You mean that…. Everyone I know, they're all….?" Shinji couldn't even finish the sentence, as Kaworu continued for him. "How did this…. How….?"

"You know Shinji this planet, Earth is no stranger to world-wide extinction level events such as this one. They help to continue evolution; after all, most creature adapt to the world via evolution and natural transformation. The human, or Lilim as called, are different in viewing this natural alteration as they seek to alter the world around them instead. They did so by creating an artificial program which could artificially be used to evolve them."

"One which was said to sacrifice old life in exchange for a new life to grow; an extinction level program device used since ancient times by the ones called the Council of SEELE." Kaworu continued, his hair wavering as he finished. "It is known by many names, but none so more as the Human Instrumentality Project as NERV has labeled this extinction ritual to be."

"SEELE…. You mean, they had NERV do…. Oh dear God, what is Rokobungi planning?!" The Third Child whispered with horror, unsure of how to truly feel about this. _A whole scenario, a whole insane plan to destroy all the human race, built for the sake of controlling the evolution of humanity? That's insane_ , he thought to himself. _Impossible even! And if NERV saw this, then why didn't they try and stop it?!_ "Wait, what about the… the Akrid, what are they?"

"Listen to me Shinji," Kaworu started once more. "When Evangelion Unit-01 awoke into its Pseudo-Evolved State, it opened the Gates of Guf; a black void of multiple colored rings made by Angels as seen in Second Impact. Through this, Unit-01 became a sort of catalyst for Third Impact or Near-Third Impact as the Lilim call it. Through this the Akrid, demonic creatures born through the remains of past animals and powerful heat sources rose from the inner form of Earth, devouring all heat and energy and reducing the population below horrific numbers. And there is simply one person to blame for this: You."

Shinji felt his heart die at the word. He did this, he'd caused all these deaths. It was his fault…. "No, no….. No, I-I didn't mean to!" He choked out with a sob, clutching the sides of his helmet tightly. "All I wanted was to save Rei! I couldn't have known all this would happen!"

"Perhaps, yet you still were the acting trigger of this."

"No th-this can't be true…." He choked out, realizing how perfectly clear his awakening and reunion with his 'friends' was. Misato didn't threaten him for no reason, nor did Asuka or anyone else with WILLE view him as evil; because in truth, this _was_ his doing. "Y-You can't truly blame me for this! Had I known this would have happened I would have stopped it….! I-I would have….!"

"I understand your feel that you cannot change what has occurred and this is indeed true; you cannot change history and yet this is the truth you _wanted_. And as consequence, Lilim now force you to carry that evil _sin_ with that choker bomb on your neck. Isn't that what it's for?"

"My… This choker is mean to kill me for my sins? How the hell was I supposed to know this would happen?! This can't be true!" Shinji cried, his emotions collapsing as he felt tears slid down his cheeks. "What have I done….? W-What have I done….?"

"I fear the other Lilim do not see it in that way." Kaworu stated, glaring forward before he spoke once more with determination. "However, all sins can be fixed and atoned for Shinji Ikari. There is still hope to change this Shinji, there will always be hope."

Shinji didn't respond, yet he mentally acknowledged this. Everything seemed to point now in his direction because of his fear of losing someone again. How could he have so blind as to not have realized it yet?

* * *

 **Command Office, New NERV HQ**

Gendo and Fuyutsuki watched as Kaworu had explained to Shinji Near-Third Impact, and how Shinji had been reduced to a sobbing form of himself. It was saddening to the older professor to see this, to see his brightest student's sons being tortured in such cruel ways. Gendo saw it simply as a sign that Shinji was not as strong and full of rage as he believed, something he would look into using in his favor.

"It would seem that SEELE's boy has spoken with the Third Child, going such great lengths to reveal the surface to him as well." Professor Fuyutsuki looked to his old companion with, saddened to see he didn't view Shinji or Shiro as his sons even now.

"I can only fear how he is handling this, and with the unknowing fear of Shiro's death and disappearance." The older man stated, frowning as he saw his younger 'friend' staring at the case which housed the Key to Nebuchadnezzar; the key to the Human Recalibration Venture. "And you are okay with this Ikari?"

"It matters not; we shall rewrite SEELE's scenario with the whole of our existence as our tool to that means." Gendo stated, eyes fixed to the metal caution case under his visor.

"And you feel than keeping your life's work hidden from your son as well as the knowledge of your elder son from him is the best?"

"I cannot say I truly believe that…." There was a time in truth that Gendo felt he should explain the HRV to his younger, to hope he'd see reason with his desire to control God and the evolution of humanity as he saw fit. But after the _other_ incident, he could not trust even that of his own blood still. _Shinji will discover the truth, soon at best_ he thought to himself, yet he still kept his doubts. _If it gets to that point, I'll simply have the clone kill him. Then I'll simple forge another and another MP so I won't have as much to deal with then…_

* * *

 **Shinji's Room, New NERV HQ**

Shinji felt so different now. He couldn't walk the same anymore, couldn't eat the same either, hell he couldn't breathe the same anymore that's how much the image of Tokyo-3's remains fucked up his mind. "Goddamnit I should have known something would happen," he murmured to himself in his self loathing pain , staring sadly to his S-DAT. "But it can't have been all in vain…. I mean I saved Rei, right? She's here, unless she really is a humanoid Dummy Plug System…."

He honestly felt like that was it; he'd fucked the Earth, everyone he once loved and cared about now absolutely loathed him, Rei was amnesiac for a long while, and God knows what Gendo was planning to achieve by using him as a tool. What was the point then anymore, living on? WILLE wanted him dead, God only knows what NEVEC wanted with him if they even did, and Gendo had possibly some sick plan with him as the major piece to it! There was literally nothing else to-

The sound of flesh slapping itself filled the room walls before returning to silence. Shinji found himself looking down to his hand, now stinging with a red glow to it. He'd... His hand made the move to slap him? Or was this a clear sign; a sign he was going insane and his own body was trying to snap him out of it.

Was that even possible, now that he thought of it more?

"Your…Your right..." He murmured to his stinging palm with a now stern glare, slowly repeating the word before he sat up fully with a look of seemingly new found determination. "If Shiro were here he'd slap the hell out of me as well, then scold me about losing my mind at such a young age... I can't let this hold me down, if anything now I have to find Rei; she's the key to understanding just what the hell's been going on and where Shiro might be. If she's going through amnesia something should have triggered those memories to return…. Maybe those books I gave her might have brought something back to her!"

* * *

 **Ayanami LCL Tank Complex, New NERV HQ**

Rei Q felt her mind was open and at ease after Shinji Ikari's arrival. It was clear that it hadn't clicked on that she wasn't the same Rei Ayanami from before the 10th Angel incident.

Though it was clear the boy could very much understand things, he was still sadly naïve at times like this. It was rather pathetic to see, how such a might fighter of the past could easily fall to a simple sight. Rei Q suddenly felt something, something different. It wasn't the LCL as it was never replenished or alternated with any unknown chemical mixtures and such, nor was it where her LCL tank was placed at. No, this felt oddly familiar.

Oddly….. Wrong. She felt her eyes slowly open, and she found herself staring at a slightly younger Commander Ikari and another woman, a blonde with a lad coat with a red and black Entry Plug labeled "EVA DUMMY SYSTEM REI"

 _What is….? Where am I?_ She thought to herself as the pair spoke to one another. _Commander…?_

" _It is simply a fake Rei; nothing more than an imitation of the original. A machine like this, able to mimic humans is powerful, and the completion of the US Devil System will create a machine unlink another." Cmdr. Ikari stated, staring to the Dummy Plug. Soon it would be only a matter of time before this would be fully developed and battle ready, which meant he had to quicken his scenario tenfold. "Have the signal pattern transferred to Unit-00 and 01. All we required is the EVA to think it carries a pilot, and sync with little to no problems."_

" _We'll have the data input into all EVAs, excluding the Unit-04 variation." The scientist stated. "But there is still the problem that we observe in the tests-"_

" _It does not matter." The Commander replied sharply. "As long as the EVA fights, nothing else matters."_

"… _.Yes sir…..We've left transfer of Unit-03 to the UN, so it shall arrive within the next few weeks. We'll have Matsushiro Base prepped for the startup and tests."_

Rei felt her mind burn more and more with confusion as to what the commander as stating, before she noticed it. She hadn't before, but now that she did her eyes slightly widened because floating in LCL next to her….

Was _herself_ , another Rei Ayanami? The other Rei opened her eyes, looking to Rei Q and spoke with a saddened tone. _"You must tell him soon….."_ She stated, before Rei Q's vision was clouded by the bubbled which rose all around her figure.

Rei Q gasped air as she felt her hands grip the metal grindings tightly, vomiting out LCL with a new found feeling of disgust and dread. Her mind now raced faster than before, with new found questions and concerns in the Commander and SEELE's scenario rising from the deeper parts of her mind. "That was…." She murmured, placing a hand to her head with confusion and fear. "That is not….. How…?"

* * *

 **Meanwhile**

 _The Rei_ here _at HQ wasn't there,_ Shinji thought with narrow eyes. _That means Gendo must have her somewhere else…. At least she read one book. But now I have to find where she is, real Rey Ayanami or not!_

Shinji walked silently through the lit hallway of NERV HQ, thinking deeply on the situation he now faced. It was clear Rei _was_ saved somehow, Near-Third Impact made that painfully recognizable; the problem now was where she was at if this Rei wasn't the real one. He'd thought for a while that she might have being held captive by WILLE at first, but the more he thought about it the more it fell apart.

WILLE clearly knew of the Dummy Plug and US Devil System's original design model were Rei and the A.I's the US built at NERV 2nd, so in truth there was no real reason to keep her. Which meant that she was kept hidden deeper in New NERV by Gendo, which was a major possibility or still trapped in Unit-01 which was more than likely the unfortunate case.

Then there was the mystery regarding Shiro's disappearance; he couldn't find it in him to believe Misato or Asuka, even if it were true. There had to be more to it than just that. He pondered on if his older sibling was in a similar predicament, being held captive by either WILLE, NERV or this NEVEC group. The case sadly ran cold as there was nothing to look into through the old MAGI system files, and he doubted this second group NEVEC would willing speak to him about his sibling with all his previous action, if they were even remotely in Japan that is.

"Hm…." Shinji hummed silently as he walked, though he didn't seem to notice Professor Fuyutsuki sitting at one of the benches. When he finally did, he stopped to give a bow of respect before starting to continue on.

"...Tell me Third Child." Shinji turned back to the old professor, a look of recognition in the old man's eyes as he spoke. "Have you ever played Shogi before?"

"Um, only once Sub-Commander, and even then I only got the rules down." Shinji admitted, turning completely to the Sub-Commander. _Just what is he playing_? The younger thought as he tried to look through the old man.

He found nothing, aside from an old man with a look in his eyes that told Shinji he'd seen things no man should, for better or worse. "That's good enough," Fuyutsuki responded, standing up. "Come lets us play a game."

* * *

 **Operations Projector Room**

"Here, I shall start without my rook, bishop and gold generals." Prof. Fuyutsuki started, gently pulling his pieces back as Shinji watched steadily. Once his opposite was done, Shinji pulled his fist up, opening it to move his piece. He felt tense and concerned and cornered, as if someone else watched not far from behind. The Sub-Commander seemed to notice this, and gave little advice to the Third Child. "Please, clear your mind; it is key to winning this game."

"You'll lose in 31 moves." Shinji winced in surprise at the notion, before giving a slight nod. He felt his heartbeat lower gently, his fist slowly opened into calm hands, and for once in a good while…..

Shinji felt truly at peace. "Alright," he answered softly, looking up to Prof. Fuyutsuki. "I am calm."

The Sub-Commander nodded, before he continued. "I should take a moment to thank you for accompanying this old man to a hobby of his."

"It is nothing, Sub-Comm-"

Fuyutsuki held up a hand, silencing the boy. "Please, here we are simple friends not commanders or fighters. I ask you call me simply by Professor or Fuyutsuki, which you desire." He stated, opening a box at the side of the shoji set to reveal a large portion of pieces.

"Very well… Professor." Shinji repeated, brushing a strand of hair to the side as he pulled his hand back to the set. "As I said before its nothing, in truth I now feel slightly more relieved with all the current stress now that I've cleared my mind."

"I see, that's good to hear. I admit I am rather timid myself," Fuyutsuki stated as the pair moved more pieces into place. "I needed this game as an excuse to speak with you."

"Speak with me?" Shinji looked up at this. This was surprising, he never took the Sub-Commander as open speakers to others about anything as he was mostly close to the Commander, especially not children like he or Kaworu and the others before NERV went to hell. "Um, what for, if you don't mind me asking?"

Fuyutsuki sighed, looking up to the boy. "Tell me Shinji, do you…. Remember your mother?" He asked hesitant, unsure if this would worked as he planned.

"Mother?" Shinji felt his heart freeze for a moment at that. That was something very much unexpected to him. He hadn't recalled his mother's face or name for a long time, possibly since the incident, and even then it was only small things like her hair color or… scent...

Yeah, ever so small weird stuff…..

"Not as much as I used to, no. I was too young then to remember her face during her passing, and Gendo went out of his way to make sure all of her belongings couldn't be touched by the outside world." Shinji admitted, looking slightly saddened by the memory of his mother passing. "Shiro probably knew of how she looked and how she was as a mother, but you'd have to ask him yourself which is, sorry to say, impossible right now."

"I figured as much; Gendo was never one to dwell in the past or recall things he feared would mentally harm him." Fuyutsuki stated, before he put forward the first piece of the truth he'd long to reveal to Shinji. The Third Child looked to see was it was; it was a photo. A photo specifically of several people surrounding a mother and her child.

Taking the photo, Shinji looked more into detail at the people in the photograph. He pointed out almost immediately the woman on the right looked eerily similar to Mari from WILLE's EVA Force, though it seemed nearly impossible. In the far back was a man, oddly similar to his father only with a barely starting beard and no glasses. Looking to the center he was a brown haired mother with another child, roughly 5 or 6 as he stared at his mother and the younger child with a smile.

"Is…. Is that…. Shiro and me?" Shinji asked, before his eyes settled on the image of the mother. That face, that smile, her hairstyle…. It couldn't be! "It can be…. R-Rei….?"

"No, that is your mother, with your older brother Shiro under you and her. Her name was Yui Ayanami." Fuyutsuki explained, a pang of mixed emotions running through his eyes. "She was student who I taught at our university before Second Impact…. And now is the control system of Evangelion Unit-01."

"W-What?!" Shinji found that absurd, no he found that impossible! A person, another person aside from himself and Rei, already inside Unit-01 _before_ either them? How?! There would have been a Near-Second Impact for that to occur! _Unless…._ "H…..H-How, Professor? How could mother be in-?"

A moment of darkness flashed as the whirling sound of faraway generators came to life. "Ah, it would seem the power is restored again. Here allow me to explain more in depth." Fuyutsuki continued, before the old projector came to life. Shinji looked to see a picture of what could only be described as a large red cross shaped carving laying like a surgical bed, the outline of Unit-01's frame in its form. "That, Shinji is the very first early prototype version of the Evangelion Control System. And it was also here that Yui proposed the idea to made direct entry and contact with cores…. Testing it herself."

"You were indeed there, though your memories have been shut out by the trauma it caused on your mental state." Shinji felt his eyes widen more than ever as the image snapped to another, now of his mother being suspended in the air by pulsing white tethers and wires, arms over her chest like a mummy.

Under her sat a pink-redish Angel like core which pulsed as she unknowingly descended into her permanent tomb, which all but confirmed it. Fuyutsuki was right. About every single damning event and motion added the nails to Shinji's coffin: the scent, the warming feeling in Unit-01, hell even the Berserk moments made sense to him now! "What happened…?" Shinji asked hesitantly, looking to Fuyutsuki.

"In the end, Yui have vanished then and there into the system, leaving only her data to be used for the future Rei Ayanami clone series." Another image came up, this time behind the old professor, revealing several heads of Rei in hexagon like openings lit up by a red light. "Both Rei Ayanami and Rei Q, the one you now know, are two of Yui Ikari's clones."

"She, Rei II, just like your mother" Fuyutsuki continued. "Is being preserved in Unit-01, and all the while a part of Gendo's sick scenario."

"Dear God, all this…. Just to see mother again….?" Shinji now realized in full just how insane his father truly was, he was willing to toss humanity to the side without a single care just to find a way to bring her back….?

"Yes, it is horrifying to see how simple the world we live in can be torn apart by our greed and lustful desires." Fuyutsuki stated, placing his pieces down till he was in a comfortable stance on the set. "Yet rebuilding it is no easy task; like time, Earth's course has already been permanently set, there is no way to alter it. Which is why Ikari is willing to make a bounty of sacrifices to see Yui once more, even if it means giving up his own soul."

"I felt it was only right for you to know part of the truth, and to understand the monster that now it your father." He finished, looking to Shinji.

"A-And Shiro?!" Shinji finally asked frantically, though he feared he knew the answer deep down. "W-What of Shiro, what happened to him?!"

"Your brother attempted a stealth operation to pull you and Rei out of Unit-01 via the Anti A.T Field we humans/Lilim and EVA can create on a solo NEVEC mission." Another image came up, this time showing an oddly built EVA trying to claw into Unit-01's opened core. The EVA had the old inner wing like shoulder pylons of Null Unit as well as a repaired head, but with dark grey repaired arms and legs.

The image flashed once more, this time revealing a large explosion which surrounded NERV HQ's pyramid top. "Though his attempt was impossible once WILLE forces attacked and destroyed the reactor of Old NERV, destroying him and his original Null Unit. Your father saw his opportunity slip once more, and so he sent Unit-01 high out of WILLE's grasp to keep them at bay."

Shinji felt his old hatred for Gendo Ikari burn-no, it was exploding inside him waiting of burst. "Gendo….." He growled, his eyes now pure of hatred as he looked back to Fuyutsuki. Then he looked back to the picture, and the memory of Mari flash in his mind. "Wait, if my mother and Rei are in Unit-01 is it possible others were able to make direct contact with EVA cores as well?"

"Yes, Unit-05 did have a person who was trapped for several years before being released out, a year or so before the Third Angel's escape attempt from the Antarctic base." Fuyutsuki admitted, pointing to the picture of the woman with glasses. "Mari Illustrious Makinami was Unit-05's soul before she was purged out, stuck in a young amnesiac form of herself before continuing to fight with NERV and later on WILLE."

"Is she… by any chance….?"

"Related to you or your parents?" Fuyutsuki finished, making Shinji nod in confirmation. "No, though she and Yui were close friends before Yui fell in love with Gendo. As such, Mari was considered Yui's sister and in turn became a sort of aunt to you and Shiro's."

 _That explains why she called me little Shiro when we met_! Shinji realized, before he stood up. _Wait a sec…. this starting to all make sense!_ "Um if it's alright with you Professor, may I borrow a pen and a notebook by any chance?" he asked, though he left before Fuyutsuki could answer. "I think I understand it now!"

Fuyutsuki felt surprise enter his old body for the first while in so long, smiling slightly at the footsteps of Shinji. "Such a painfully horrible role I play in this act, dear Yui." The professor whispered, looking above as if for a sign that she understood his guilt and regrets. "I'm truly glad to see your sons push to discover the truth, even if close to impossible. I only hope this is what you wanted….."

* * *

"The final covenant's time slowly draws closer," Gendo stated, looking forward to the decapitated head of Lilith, sitting on a mountain of failures and corpses, an eerie smile under its eyeless sockets. "Yui, we shall meet again soon."

He brought the metal caution case up, placing atop his old observation desk and opening to see the Key. Still in perfect condition as ever; all it now took was someone to truly activate it. "Such a dark reminder of our past as a species, you are..." Gendo uttered with a twisted smile of lust and oh so growing desire as he pulled it out and held it into the light, the yellow glass shimmering with the human system inside. "Nevertheless you shall be my key to the Chamber of Guf, and the power it holds."


	7. Chapter 7

_**Neon Genesis Evangelion, the End of Evangelion, and the Rebuild of Evangelion are owned by Hideaki Anno and written by Yoshiyuki Sadamoto. I own no elements from the original Manga, TV show, or Rebuild and EOE films but my OC's.**_

 _ **That said, Please Enjoy The Show!**_

Talking-"Hello"  
Radio/EVA Voice-" _Hello_ "  
Thoughts- _Hello_  
VEELE/VEELE Clones-" _ **Hello**_ "  
A.I-" **Hello** "

* * *

 **Chapter 7: Pieces of a Larger Puzzle**

 **Shinji's room, New NERV Headquarters**

Shinji quickly wrote into the book he'd taken from the library, muttering to himself as his train of thought rocketed all around his head. Since his Shoji game with Fuyutsuki, he'd been trying to piece all the parts together and for the most he had it with only few parts still unknown to him. He'd pretty much ripped apart the MAGI system files for historical events and old records dating back to the beginning of time, to First Impact and back just to put together his belief in the truth.

He took anything he could find, anything! Things he hadn't known about NERV or NERV 2nd Branch, Lilith and Adam's Black and White Moon, Evangelion, all of it. At least, the most he could recover.

First he put the knowledge of Adam and Lilith who'd crashing into Earth billions of years ago, creating the First Impact. Both had two spears, one of Longinus and another dubbed Cassius. Both apparently had gone into a sort of Angel-like hibernation as Adam's Angels were scattered and looking more than likely for him.

At some point in time Shinji and Shiro's mother Yui Ayanami Ikari worked with Mari Illustrious Makinami under Professor Kozo Fuyutsuki in the university when she met their father Gendo Rokobungi. At some point they both were infatuated with one another, got married and had Shiro.

He quickly skimmed through from there to the Katsuragi First Contact Experiment in Antarctica, where Adam awoke when combined with human or Lilim DNA. That was where it got slightly different, as this was where SEELE got into the act. It was clear SEELE had a lot of behind the scenes deals and work in certain parts of history, so it wasn't out the window to assume they had some help in creating Second Impact.

After Second Impact, Shinji was born and a few years later Yui and Gendo worked with Ritsuko Akagi's mother, Naoko Akagi along with Fuyutsuki to construct Project Evangelion with the data recovered about Adam from Second Impact. Yui was then pulled into the test type Unit-01's core and became the Control System, with Gendo completely losing all passion and emotion to his sons.

Gendo then had Shiro send to NERV 2nd branch and had Shinji sent to his brothers, and where things got different.

 _Really_ different.

At some point in time Gendo had created Rei Ayanami from Yui and possibly Angel DNA to probably sooth his pain or guilt, or something Shinji didn't really give a shit about for obvious reasons. Later on he then built the Dummy Plug system, though didn't use it was it was still under tests and experimentation. During that time, SEELE got Gendo into something called the Human Instrumentality Project, with Gendo working secretly behind their backs with his own plan to use Third Impact to bring Yui back from the dead.

During that time Mari went searching for answers regarding Evangelion and the Angels possibly at the Antarctic base Bethany base where she was either accidently pulled or forcefully purged into the mysterious EVA Unit-05, before she came back much younger and slightly amnesiac.

Meanwhile, Shiro was trained to pilot EVA at NERV 2nd Branch as the US built Unit-03 and the DEVIL System for NERV HQ. Shiro was later placed into something dubbed the Human Insanity Experiment, which much to Shinji's concern was where he met VEELE or Vincent Versailles Keel as he was originally called. A few years in that time and the pair apparently separated when Shiro was permanently placed as the pilot of Unit Null when VEELE was viciously injured during a sync which mentally damaged him.

For the most, everything was pretty much already known to him: Shinji was called to Tokyo-3, met Misato and a few others, made the pilot of Unit-01, fought the many Angels of Adam, met Rei, reunited with Shiro, met Asuka and VEELE and his aunt Mari after she'd apparently killed the Third Angel, fought the Tenth and finally started Near-Third Impact.

That's where it got more blurry. It was clear that NERV had some sort of uprising after God knows what, maybe the Akrid rising built some sort of rift which made WILLE and NEVEC form. Or maybe Misato found something and Shiro didn't like her means to stop NERV and SEELE, he didn't know.

For a while the Third thought of questioning this other Rei, Rei Q as she was dubbed by Fuyutsuki in the previous conversation. But now he realized if he did he'd possibly have another breakdown, so he passed the idea aside. Though he knew there would be a time where they'd speak, and he'd have to make the choice whether to help her or leave her to die... Shinji finally sighed. "The only way I might get my answers sadly is if I play the role in Gendo's sick game. Not much of a choice in that..." He murmured in annoyance, cracking his neck with a groan of relief. "That's better, now I'm mentally wasted with info and crap…. I need food!"

* * *

 **Unit-13 Pod, New NERV Headquarters**

Gendo and Fuyutsuki watched silently as Unit-13 was pulled steadily out of its pod, blood flying around the pair like rain as the silent Type-13 Evangelion finally halted above the pod opening. To be truthful Gendo had originally wanted the Third and Fifth Child to enter the pod and then Unit-13 directly due to concerns regarding its original template and... Test pilot. "It seemed Unit-13 finally draws silent Ikari." Fuyutsuki noted, looking up to the large behemoth of an Evangelion with blood dripping off its dark figure.

"Indeed, the final executor is complete and the beast within has been tamed for the time being." Gendo stated, eyes sternly staring for any twitched and waiting to hear the sharp roar of its vocal cords. He found nothing, just a silent Angel-like humanoid hybrid that would continue SEELE's scenario and his Human Recalibration Venture. "Time is now of the essence; I have no doubt NEVEC will be raiding this place soon."

"Should we activate the Mass Production Facility and Dummy/DEVIL Command Center then?"

"No, this place will be lost by then. And all the pieces have been reclaimed…. It's time Fuyutsuki."

"I shall prepare preparations for departure then." Fuyutsuki stated, turning to make his leave. As he did, he looked back up to Unit-13 as it was pulled higher towards the roof opening with sadness. "I'm sorry…."

* * *

"You want me to… Pilot again…?" Shinji asked with slight concern as Kaworu nodded. He sighed, taking a seat on his bed as he laid back. His albino friend had come asking him to once more pilot with him, though Shinji felt it was more as an order than a asking. "I… I don't know Kaworu…. I mean…. The last time I piloted I nearly destroyed all of humanity…. I…. I can't go through that again…."

"Shinji, please understand that the problems done by EVA can be fixed by EVA." Kaworu tried to reason, looking at Shinji's recording book before placing it down.

"I know that but…." Shinji trialed before finally letting out his fear. "I just can't trust anyone anymore, you know?! I can't trust Gendo, or Misato or EVA or anyone or anything anymore! And I'm scared I'll just ruin the world even more, I-I can't put these people through that hell again!"

Kaworu frowned. It was clear the reveal of Earth and betrayal of the Lilin were too much for Shinji, even if he played it off as he wasn't bother by it anymore. And with what WILLE and Ikari had done to him, the Fifth could understand Shinji's mistrust in people; if only he could help Shinji to truly understand what they could achieve, just them and no others to command them. "But Shinji," Kaworu continued. "You can trust me."

"I…. I don't know any more alright?! There I admit it, and I'm sorry to say it, but I don't know if I can trust you too!" Shinji finally yelled out, slamming the back of his head onto the wall. He felt his emotions building up again, and he choked back a cry before continuing. "Besides even if I wanted to pilot I'll be dead the moment I step into one…. Misato and WILLE, they…. They put this damn choker, don't you remember? That's my sin, they said it'll kill me if I ever pilot again."

Kaworu simply watched Shinji let his head fall forward with a tear escaping his eye, before the Fifth Child finally walked towards silently him. "I just…. Can't lose any one because of EVA anymore…" Shinji tried to explain, but that was washed away with shock as Kaworu placed his hands to the choker sides. In an instant the choker gave a beep and pulsed red as it unlocked, with Kaworu steadily taking it from the Third's neck.

"I understand Shinji," Kaworu stated, taking the choker up and to his neck a Shinji lifted his head with a gasp. Kaworu placed the choker around his own neck, with it giving a final beep as it locked once more. "For you then, I shall shoulder your burden of Lilim's curse and the risk of the EVA awakening alongside you."

"Kaworu," Shinji gasped out, shocked to see his friend go to such great and risky lengths for him. It was clear Shinji meant something to Kaworu, something more than just a friend. "….Why? Why take my burden?!"

"Do not worry for my, Shinji." The Fifth Child answered with a reassuring smile, taking a seat beside his brother in arms. "The Lilim actually made this choker because of their fear of _me_ , so it was only a matter of time before I took it from you."

"Listen to me Shinji," he continued. "Your only hope is the Lance of Longinus and Spear of Cassius locked away in Terminal Dogma ever since the NTI, as they are the keys to the Human Instrumentality Project. But if you and I take the spears with Unit-13, NERV will no longer have a means to create Fourth or Final Impact and we will have a means to repair the world."

"I…. I think I understand now." That was something Shinji hadn't understood till now. Longinus and Cassius clearly had some sort of major role in the Angel history, but it not made a sort of sense. The spears stood as a sort of Yin and Yang, able to destroy and repair things with their power. If that was the case, then the lances could truly be able to redo what he caused, he could fix everything! Shinji finally smiled to Kaworu, a slightly rush of adrenaline coming back to him. "Knowing you, I know it's possible you can do it!"

"You mean _us_ , Shinji." Kaworu corrected, raising Shinji's confusion. "Allow me to explain: Unit-13 unlike its predecessors using a new Double-Entry Plug System, allowing there to be a pair of pilots rather than just one. And because of that we can become the hope of Lilin together, and finally fix your sin."

"You really mean that?"

"Of course. What you need right now after all is hope, with atonement and composure at your side as well."

"I… I'm at a loss for words Kaworu, you're amazing!" Shinji complimented, looking to his friends crimson eyes. "You seem to know everything, a not just simple things like fixing the S-DAT and stuff. You really seem to be philosophical in a sense with a general friendly vibe, and that gives me an odd sort of reassurance."

"That's only because I'm thinking about you." Shinji felt a light blush and his heart flutter slightly at Kaworu's comment, somewhat shocked by it and yet oddly happy to hear that. He didn't know where this feeling came from, but he most oddly accepted it.

Kaworu simply smiled and stood up, holding a hand out to his friend. "Besides, think of piloting Unit-13 as playing the piano in a sense." Kaworu reassured his friend as Shinji took his close friends hand and stood alongside him. "Great things will come should we do this Shinji, I promise you that."

"Yeah, I guess they will." The Third Child replied, smiling to his friend. "Let's do it."

* * *

 **Central Shaft Tunnel Entrance, New NERV Headquarters**

Evangelion Unit-13 hovered above the now opening center shaft. Compared to his previous Unit-01, Shinji had to admit the EVA came from major similarity in design. The EVA possessed a whole purple color scheme, with black, red, yellow, and green linings or designs all across the body. It housed now 2 pairs of yellow eyes which seemingly connected to the glowing lining that traversed to the back of its head.

Unlike its predecessor, however, Unit-13 was taller than the original EVA Series as well, and topped off with the new Dual-Entry type Plug System. The Third pondered on the possibility of there being another Soul in Unit-13 as he and Kaworu fixed on their plug suits, a sort of bridge to help fill the gap where the pilots could not during sync. Though he tossed the idea out, he kept it in the back of his brain. If his mother was in Unit-01, someone else was more than likely forced into this once too. Though, he'd keep quiet for now. Best not to attract unnecessary attention.

Shinji felt the Entry Plug spin into the EVA's back side, though he didn't look to see the activation sequence as he stared down to his S-DAT. This was all he really had to remember his family, to remember Rei and all his friends before Near-Third Impact. But with Kaworu and Unit-13. He'd fix all that. _Soon we'll fix all that,_ he thought to himself as the sequence finished to reveal the Fifth Child in a control seat next to him. _I promise, Rei. And then I'll find Shiro and together the three of us will find a way to get you out of WILLE or Gendo's hands._

 _I promise._

Both the Third and Fifth Child smiled to one another, before both turning to the task ahead. "Evangelion Unit-13," the pair spoke in unison, the large EVA's eyes pulsing to life. "Launch!"

* * *

 _"Signal detected!"_

"New NERV Evangelion detected!"

"Ikari's already playing his card then…." Captain Katsuragi murmured, glaring at the emergency hexagons all around the bridge. _Then the Specimen has fallen once more into Ikari's sick web of lies…._

"Captain, I'm detecting a massive horde of Akrid moving around the old Geo-Front!"

" _Large Thermal Energy signature detected, moving at rapid speeds towards Tokyo-3! It's the Stormbreaker!"_

"Full power to the engines, now! We have to stop NEVEC before the Akrid can stop us from getting to Terminal Dogma!" She snapped, lifting the choker detonator into her field of vision as the Hirnstamm Tower lifted with Wunder slowly turning. She felt her stomach waver at the memory of the Specimen dying before her and the others, though she forced it away _. It's for the greater good_ , she thought in silence. _That's all it ever has been, for humanity to live we have to make sacrifices and damn the damned who caused all this…. Right?_


	8. Chapter 8

_**Neon Genesis Evangelion, the End of Evangelion, and the Rebuild of Evangelion are owned by Hideaki Anno and written by Yoshiyuki Sadamoto. I own no elements from the original Manga, TV show, or Rebuild and EOE films but my OC's.**_

 _ **That said, Please Enjoy The Show!**_

Talking-"Hello"  
Radio/EVA Voice-" _Hello_ "  
Thoughts- _Hello_  
VEELE/VEELE Clones-" _ **Hello**_ "  
A.I-" **Hello** "

* * *

 **Chapter 8: Angel Grounds**

 **Central Shaft Tunnel, New NERV Headquarters**

Almost immediately Unit-13 gently and silently began down the large shaft. The Geo-Front, while suspended high in the air now, connected New NERV HQ to Lilith's chamber via large metal shaft. Shinji couldn't help but feel tense by the descent though, he felt anxiety fix its way up his throat and his chest tighten more than before.

The last time he piloted an EVA he nearly destroyed the human race and Earth, who was to say it wouldn't happen again. _No...No! It won't happen again!_ He thought to himself, looking to Kaworu who looked downwards on the opposite hemisphere. _With Kaworu piloting with me, I should be able to control the EVA slightly without taking full control. Which means it won't go berserk unless-_

He cut himself out of his thoughts as he noticed a familiar yellow metal shoe and ankle, glancing up to see Mark.09 holding the cable Unit-13 road down. "I uh, thought it was just us Kaworu..." Shinji murmured, looking away as the Fifth Child looked to his sibling-like friend.

"Who, you mean Mark.09? She's only here to support us it WILLE EVA Forces arrive, nothing more or less." He explained, making Shinji simply sigh in annoyance. "What's wrong?"

"Well, while I am grateful she's here to help us," Shinji started, not bothering to realize the communications window with Rei Q in Mark.09 was open. "I was really hoping it'd just be us you know? Besides, I don't think WILLE would launch an assault after the apparent last raid they tried to accomplish."

"That is true, though you must admit the Second Child is very... Unpredictable." Shinji chuckled at that softly, giving a nod as they continued down. The further they went the darker it got, till they finally reached the end of the metal shaft. Shinji glanced back to Rei Q's Mk.09, feeling a sort of pity for the Rei clone. He knew he should probably explain that he knew who or rather what she really was, but didn't feel he was at the right moment to. Perhaps once the world is fixed he could tell her, and hopefully explain how and why she was created for Rokobungi's sick game.

 _Perhaps later,_ he thought to himself. _Right now I have to focus…._

Lights on Unit-13's cheek armor flashed to life, revealing a twisted image to Shinji. "Oh dear God…." he murmured, looking at the many blood red silhouettes that were seemingly painted onto the wall. 'What…. What is all this….?"

"Ah, yes those are the Failures of Infinite." Kaworu stated, brushing off the imagery beforehand. To him this was not new, but rather as basic as the sky since Near-Third Impact. He glanced to a still surprised Shinji before looking back down to the darkness. "It's nothing to worry about."

The darkness seemed to welcoming more than ever, revealing a large chamber pitch black. As they lowered more, Kaworu began explaining what the chamber was. "Here it is, Lilith's chamber, having been closed off by WILLE and NERV from the outside world for the past 14 years. This will be like opening a lid, in a sense, though for this we'll have to be in perfect sync and harmony with Unit-13."

"We can do it together." Kaworu said with a smile, causing Shinji to return one to his friend.

"Alright, let's do it!"

From the front center between the seats came a machine which connect the pilots to Unit-13, which hummed gently to life with pulsing eyes. "Remember, clear your mind and watch your tempos; it's just like the piano duets from earlier."

Shinji nodded, shutting his eyes with concentration. He felt himself grow clear of everything he feared; he felt his mind open more than ever, even more than when Prof. Fuyutsuki spoke with him about Unit-01 and his mother and Rei. In the center of the pair's large screen, the hologram of the shaft revealed a set of word. _Here we go,_ he thought. _For Rei, for Shiro, even for Misato, and most of all..._

"Let's do it, Shinji," The Third Child opened his eyes, now full of determination.

 _For mother._

 _ **Monitored Target Object**_

 _ **FINAL CONTAINMENT SEAL**_

 _ **Bottom most level of Central Dogma**_

 _Here we go,_ he thought silently, praying this would work.

The ground below Unit-13 reflected like water, before a groundbreaking act was played forward. The ground collapsed into large cubes which moved away with anti-gravity like forces, opening till the hole was larger than both Evangelions and as wide as the main shaft from before.

"We did it!" Shinji cheered with a grin, making Kaworu smile back with happiness. The opening continued till they finally came upon another chamber.

"Here it is: the lowest level of NERV's Central Dogma." Kaworu stated, his face stoic and stern with a now serious glare in his eyes.

"And the epicenter of Third Impact…." Shinji finished, looking below to the large chamber the Second Angel once slept in. The once bright orange LCL lake was now filled or covered by hundreds upon thousands of EVA sized human skulls. Atop the skulls sat Lilith's cross, now grounded with a large object not far from it. The object was a larger person, or rather corpse, almost 80 times the size of Unit-13. It had the physical body of a female attempting to crawl away, pure white skin with large red openings on certain parts. The head was seemingly ripped off, with one arm reaching out as if to grasp something.

"Is… Is that Lilith, the Second Angel?" Shinji murmured, shock eyes by the giant corpse.

"Yes, you're looking at her corpse." Kaworu explained with a grim look as they lowered, revealing them to be a good distance from the large body.

"My God, this is what Misato and the rest of us tried to protect then…." Shinji spoke to himself with a glare of his own, unsure of how to fell. He felt regretful and somewhat grateful the Near-Impact killed the Angel, as it seemingly halted any Angel assaults, if any now, from before. He watched the corpse, before noticing something sprouting out Lilith's back. "Wait, isn't that the Mark.06?"

"Yes, and my previous Evangelion as well," Kaworu replied, looking to his past vessel. The EVA was now 3 times Unit-13's height, completely white and halfway submerged into the back of Lilith's while clutching two red prongs that dug into its chest. "The Lilim modified it to act autonomous, and this is the result of it."

Unit-13 let the tether it held loose, feet crushing the skulls on impact with a robotic growl. "I'm guessing those two red prongs are our target?" Shinji suggested, looking at Lilith's corpse and the large needle like prongs jutting out of the old Mk.06.

"Yes," Kaworu replied looking up with a slight smirk. "Longinus and Cassius, they're the key to fixing Near-Third Impact. And with the Dual-Entry System, our souls will be enough to pull them out."

"So wait, if you can do it me" Shinji glanced up to the Mark.09, feeling Rei Q's saddened stare looking him down. "Couldn't you do it with Rei Q?"

"No, to use both spears both pilots must be pure Lilin, not _clones_. Though her soul resides somewhere else." Kaworu stated, red eyes fixed on the center corpse of Central Dogma. "Alright, let's begin."

Evangelion Unit 13 started its walk over the human sized skulls, bone cracking and collapsing under the metal pressure while Mark 9 stayed back. As it moved, Shinji started with interest at the form of Lilith and the Mark.06, which gripped the Spears of Longinus and Cassius in both hands. He pondered though in question as to why no others like WILLE or NEVEC or even NERV had come this far below since Near-Third Impact to try and remove the spears, and why they'd went to such great lengths to protect it if the Angels were all dead?

 _It can't just have been because of Gendo._ _Maybe because of the Akrid_? Shinji pondered mentally. _Can... Can they too be clones of-?_

"Wait," all of a sudden, Unit-13 stopped as Kaworu noticed something. "Something's off….."

"What's wrong, Kaworu?" Shinji's question was answered with silence, Kaworu placing a hand to his chin in a studying way. His eyes traversed to the spears, as if concerned by their appearance all of a sudden.

"Odd….. The Spears seem identical. Almost _too_ identical," Kaworu murmured. "And they're placed in an oddly similar formation-"

"... Look, let's just grab the Spears and leave alright?" Shinji asked, impatience surpassing his confusion. "Isn't that what we came here for anyway- ACK!"

Unit-13 was cut off by an explosion which engulfed its figure, the RS-Hoppers from the left shoulder pylon rushing to block it out. The smoke was forced apart by from the impact of Unit-13's A.T Field and the object, a familiar red and black Evangelion.

"It's Unit-02!" Shinji gasped in shock, a very dreadful feeling of its pilot staring him down. "Damnit, its Asuka!"

Blades met with Unit-13's AT-Field, letting sparks fly from the both weapons as Unit-02 pulled back with a glare. Its Gatling gun had been replaced with a more Evangelion like arm, but it still stood out as it was slighter bulkier than the original. "Shinji you damn brat!" Asuka yelled his name out with venom. "What the hell are you doing?! You're not in that damn EVA are you?"

Unit-13 gave a slight growl as Shinji's eyes narrowed in anger. "Yes, yes I am and I'm going to fix the world with it!" He exclaimed, slowly pulling Unit-13 back around towards Lilith's corpse. "So don't try to stop me!"

Asuka gritted her teeth; she hadn't wanted to fight. But if this Shinji was going to be a brat, then she sure as hell had a reason to put him in his place! "You damn brat, you want to help?! Then stop piloting!" She yelled, rushing forward.

Unit-02 Dash rushed forward, but went sailing back as Mark.09 rushed forward. The orange and white Unit-00 clone jumped into the air, ready to slice the red EVA's head clean off, that is still an explosive round crashed into its back. "Goddammit you are always late with your support!" Asuka growled out, rushing forward.

"Oh calm down, Princess at least I'm not back on Wunder." High above at the entrance point sat Unit-08, rifle in hand as it fired down onto the Vessel of Adam that was Mark.09. "A Vessel of Adam, huh? Well, the least I can do is stop you from getting back up!"

Unit-02 Dash rushed forward with its dual blade, trying to cut through the A.T Field. The RS Hoppers, sadly, give a god job at keeping her at bay as Unit-13 watched almost in amusement. "Stop Asuka, why are you doing this?!" Shinji asked with annoyance, looking with his EVA to Unit-02 as if tried cutting into the A.T Field. "Don't you get it? Those spears are our last hope to fixing this, don't you want the Earth to be fixed?!"

"If you want to start fixing the world, then _stop_ piloting the damn EVA, brat!" She yelled back, pulled at the controls as Unit-02 was pushed back by the RS Hoppers. "Christ almighty, Shinji you'll just make things worse!"

"I will not!" Shinji screamed back, the RH Hoppers just barely holding Unit-02 from Unit-13. "How can I make you understand, with those spears we can fix Earth! We can save everyone again!"

Asuka pulled Unit-02 back, and she couldn't help but feel disgust and pity for Shinji, if it was Shinji that is. His desperation for saving Rei killed almost everyone on the planet, and he willing to go all in with Fourth and Final Impact to fix it!? He'd just ruin Earth more! _He's truly willing to damn us all to death just so he can be viewed as the innocent one in this?! That…. That on its own is just unbelievably pathetic,_ Asuka thought before speaking up. _Even if you aren't the real Shinji Ikari, why can't you just accept it and deal with consequences?!_ "You are so damn naive for a brat…." She murmured, but that sentence dug deep into Shinji's skin.

Shinji felt his heart beat fast with newfound hatred at Asuka. How dare she, someone he went out of his way to save, call him naive for trying to fix everything?! "You… You! How dare you call me naïve!?" Shinji finally snapped, Unit-13's mouth bolts cracking as it let out a louder growl. "I'm tired being nice, just that just doesn't work! I tried asking what happened so I could know where to start fixing, but you couldn't just give a straight fucking answer! I wanted to help, but you strapped a bomb to my neck! No, I am not naive Asuka! Your clueless, in the end WILLE's no better than NERV! You just don't get it!"

The RS Hoppers slammed inti Unit-02, sending left and right as the A.T Field popped up at random. Shinji huffed, forcing hair out of his line of vision. Never in his life did he think he'd yell like that again, and to a person he once considered a friend. He sighed and looked to Kaworu, a hint of concern in his eyes and voice. "What the hell's so wrong, Kaworu?"

The Fifth Child didn't respond, continuously looking to the spears atop Lilith. "Those spears…. Yes, we need them but…." He murmured, looking up with a spark of realization in his eyes. "Yes, I get it now, Bastard Lilim!"

Another explosion tore apart the ground surround Lilith's cross, though Mark.09 was unaffected as she'd taken to using the cross as a shielding. "Hey… Hey, SEELE fill-in pilot!" Rei Q looked up, barely catching the thin barrel of Unit-08's rifle. "You should probably get out of that Vessel before it goes all crazy on us, you know?"

"I… I cannot." Rei Q felt compelled to simply say no, but she felt a pinch of…. Hesitation? Never had she experienced such a feeling, and this was no simple feeling either. No, this felt more as if was very familiar to be near. "I was not ordered to leave my Mark.09."

"God, you're so straight-laced." Mari replied, fixing her glasses before firing another round. "Your original was nothing like this, you know?"

"The original? So it is true, I am clone of Rei II and Yui Ayanami….." Rei Q murmured, unsure of how to really respond to such a thing. Even with Shinji's reassurance, she recalled the memory of the other Rei in her episode then and feared the worst. Had she been a defect, a broken model that required such emotions as sadness or anger and happiness? Or had the original simply grow accustomed to these emotions when closer to other Lilim?

Unit-02 jumped high and fast, trying to cut into Unit-13's frame. The Unit-01 descendant simply jumped back, but lost footing as the skulls it landed on were too weak to support its weight. The EVA tilted back as Shinji cried out in shock, and not a moment later did Unit-02 managed to finally destroy the RS Hoppers.

Unit-13 pulled its arm up to protect itself at the RS Hoppers exploded, shaking it and the pilots. Shinji clutched the controls tightly, looking to Kaworu who seemed to be realizing something drastic. "Kaworu, what's wrong?!" Shinji finally cried out, but his friend simply continued looking with concern and fear in his eyes.

Asuka screamed with fury as Unit-02 jumped up, the dual blade broken in two now dual swords. Unit-13 swung its arms, catching the blades with bare hands as sparks flew from either side. "Asuka, please I'm begging you!" Shinji finally pleaded, fighting through the pain in his hands and bubbling LCL. "Please, don't do this!"

"Just shut up and take your punishment, you brat!" Asuka screamed, forcing her EVA beyond its previous limits. The blades slowly dug into Unit-13's hands more, but before more progress could be made Unit-02 gave a whirl of depletion, eyes and Entry Plug shutting down.

"Oh, you're kidding me Unit-02!" Asuka cried out to her EVA, before turning to the communications window. "Four-Eyes, I need a spare fast-!"

Asuka was cut off when Unit-13 finally rose back up, backhanding Unit-02 across the white plain. Shinji breathed through his mouth, finally sighing before looking towards Lilith. _Finally, no more stupid distractions!_ He thought. "Now's our chance, let's get the spears and leave!" He called to Kaworu, though he didn't wait for an answer.

Unit-13 turned to Lilith's corpse, walking steadily up towards its large form. That is, until Kaworu finally spoke up. "We… We should turn back Shinji," He spoke with fear and the sound of exhaustion, a hand over half his face to hide his fear. "I have a bad feeling about this…."

Shinji felt hair on the back of neck straighten up at Kaworu's statement, and he turned to glare at him. "You can't be serious Kaworu, after all we've gone through to get them?!" He asked, trying his best hold back any anger. "How could you want to just throw it all away when we're this close?!"

"You-You don't get it…. For Lilith sake, those _aren't_ the spears we need!" Kaworu cried out, but it clear in his mind that Shinji wouldn't stop. SHinji's mentality remained on the single hope that Longinus and Cassius could fix it all of this; the problem was he was to blinded by his ambitions to realize they _weren't_ the right spears.

"What?! They're not, but how?!" Shinji grunted his teeth as Unit-13 crawled higher, closer to the Mark.06 and the spears. He really had hope Kaworu would stick with him though and through, but in the end he was still on his own against the world! "You're the one who told me we needed the spears! For God sake Kaworu it's the only reason I'm even in this damn Eva!"

Shinji finally pulled on the controls, separating the sync with Kaworu. Kaworu looked up in disbelief as the center machine flat lined with a final warning beep, his control seat veering slightly to the side as Shinji switched all control to himself. "T-The control system!" Kaworu exclaimed, fearful at Shinji's intentions.

Unit-13's once yellow eyes now pulsed crimson red, a dreadful sign that Shinji now had fully taken control over the Evangelion. "I'll take Longinus and Cassius, for Kaworu, for Shiro and everyone else!" Shinji exclaimed, raising his head to look up at the spears. "Then the world will be restored. And even Misato will…!"

Slowly, Unit-13 stood before the large Mark.06 pulling itself slowly towards the EVAs shoulder pylon to climb up.

"Oh God, no!" Asuka gasped in fear, watching as the Unit-01 copy climbed atop the Mark.06's chest, directly in between both spears. "Four-Eyes, I've cleared the RS Hoppers. Use of A.A bullets granted!"

"Finally! Moment of truth!" Mari called with glee, loading her rifle with Anti Air rifle shots. "Here's my ace in the hole!"

The bullets buried into Unit-13's shoulder blades, but to Mari and Asuka's horror they simply faded through the EVA. "T-There's no A.T Field…?" Mari whispered in surprise, watching through her scope as the red circles on Unit-13's chest began to glow red. "T-That Evangelion… It's… It can't be…?"

The chest of Unit-13 finally burst to reveal another pair of arms, slowly raised into air as if in a sign of pure, dark control over the chaos that was Earth. Shinji grunted, tugging at the controls as both pairs of arms grabbed either spear. The spears groaned through the metal that it scrapped, sparks flying as they tilting left and right while Unit-13 slowly pulled at them.

"D-Don't do it Shinji!" Kaworu pleaded with fear, clutching his face with horror as Shinji's grunt grew louder.

"Stop it, you brat!" Asuka screamed through the comms, but no one seemed to notice the occurrence _underneath_ Unit-13. The Mark.06's colors began to fade back, its head slowly looking to see Unit-13 as its visor pulsed red with a familiar angelic growl.

Shinji blocked all sounds and faces out, everything was blocked out as his eyes flashed crimson for a split second. Unit-13 in turn, with one fell swoop, ripped the spear out with a scream of fury from Shinji, slamming both spears together above itself like they were a symbol of hope.

Shinji looked up with a look of desperation mixed with happiness, watching as the spears altering into a pair of Lance of Longinus'. _Yes!_ He thought to himself. _All will be right with the world with-!_

And just like that, the Devil returned in Unit-13's form.

Only now, there was less and yet so much more as stake.

In an instant Unit-13 began hovering in the air as it lowered the spears beside it, the body of Lilith finally expanding like an over inflated balloon before exploding into a wave of blood with completely covered the once white plain. Shinji blinked, squinting to try and look past the blood as he recognized an object floating in the red lake. It wasn't Mark.09, or Unit-02 or 08, but rather a EVA in similar design to Unit-01 with two horns, a dark blue and yellow color scheme to it and a slghtly more organic look to its frame. "It's EVA Mark.06?" Shinji questioned, before a terrifying alarm blared to life. He looked to his side to see a Blood Type hologram come up, eyes widening as he read there was a Pattern Blue in the vicinity. "B-Blood Pattern Blue? But that's impossible!"

An angelic growl echoed all across Lilith's chamber, and Shinji looked in horror to see the Mark.06 staring at Unit-13 as it spun on its side steadily, its visor pulsing with some sort of distortion behind it. Shinji's eyes widened in horror as the Mark.06 was slightly nudged by a pulsing halo above it, its body slowly beginning to return to life as Unit-02 attempted to intercept its awakening. "Crap the 12th Angel's still alive!" Asuka screamed in anger, Unit-02 rushing forward as it switched its previous arm for weapon of more... firepower. "We have to stop it from waking up!"

The mark.09 as well attempted to cut off the mark.06's head, but the EVA abruptly dodged either Evangelion's attack, rising with a horrifying Angel screech. "This is not possible…." Rei Q murmured, unsure of how the scenario was supposed to act out now.

"What's happening, its like the 12th has a mind of its own?!" Asuka inquired as Unit-02 finally readied its mini gun arm. The EVA fired rounds all around the Mark.06, but they didn't make contact as an A.T Field rushed to life. "Damn it, don't tell me this part of Gendo's plan or something?!"

"I don't think so," Mari called out, reading the newly recorded scan from the DSS Choker: nothing, at least nothing world threatening. "Though something tells me we just opened a bad can of worms..."

* * *

 _ **A/N: Finally, no more stupid freaking tests! That's right, I finished that EOC Reading crap and now can focus on smaller school problems like classwork and this story. Now I won't lie it will be while before Chapter 9, so please be patient and let me know what you think and hope to in the story for the future.**_

 _ **That said, this is KnightOfZ3R0 signing off!**_


	9. Chapter 9

_**Neon Genesis Evangelion, the End of Evangelion, and the Rebuild of Evangelion are owned by Hideaki Anno and written by Yoshiyuki Sadamoto. I own no elements from the original Manga, TV show, or Rebuild and EOE films but my OC's.**_

 _ **That said, Please Enjoy The Show!**_

Talking-"Hello"  
Radio/EVA Voice-" _Hello_ "  
Thoughts- _Hello_  
VEELE/VEELE Clones-" _ **Hello**_ "  
A.I-" **Hello** "

* * *

 **Chapter 9: The Escape**

 **Undisclosed location, New NERV HQ**

"The time had once more returned to reenact that of the Dead Sea Scrolls," Gendo stated to the Council of SEELE, a seemingly emotionless farewell to the eyes of Earth. It seemed almost ironic in the sense that he and Fuyutsuki were the ones who helped SEELE start this sick evolution project, and now they would be the ones to pull the plug. Literally. "And now we say farewell."

Fuyutsuki silently listened as he began shutting off the connection from NERV to SEELE's monoliths one by one, first disabling SEELE 04 as Gendo continued. "Though you may have alternated and transferred your souls, you can only be able to cheat death as you have been gifted with the fruit of knowledge."

Off went SEELE 06, the rest simply listening in silence as they awaited their inevitable deaths. And yet they so happily accepted it, for they knew their mark on the world would spark a new life which would give the human race a chance to go one forever more. "You may very well be able to remain immortal for eternity, but like as I said before, you like the rest of us cannot evade death when it comes for you."

SEELE 03 went silent as it shut off. "You have assisted us in our evolution since the beginning of mankind's birth, and with your burden of immortality gave us the sophistication of civilization." Gendo continued as Fuyutsuki disabled SEELE 05.

"On behalf of all of mankind and those yet to come, I am deeply grateful for your sacrifice to us." SEELE 06 shut off, leaving only SEELE 02 and 01 remaining. He knew they both in a sense feared what Gendo was planning, but he would assure that their scenario would not alter even in the slightest.

"With your falling into death hand, we honor your deaths with their reunion to their rightful placing." SEELE 02 did not speak, thought Gendo knew he glared behind his monolith as it went silent, leaving only Keel and Gendo alone.

"I assure you, Lorenzo Keel that the Human Instrumentality Project and deed you've long sought co come to fruition shall be carried out." Gendo finished, looking to SEELE 01 as he spoke. "Please sleep with everlasting peace."

" _Our wish for mankind has all but already come and gone to pass, Ikari."_ SEELE 01 explained. _"And behold the world of tomorrow has been reborn anew. May the instrumentality of humanity and purification of all Lilin souls come with peace. Yes, all is now right with the world."_

And like those before him, SEELE 01 fell silent, its monolith like the Council now nothing more but stones with simple markings on them. "Fuyutsuki, come. We haven't much more let do accomplish." Gendo stated, turning to make his leave with his colleague behind giving one last glare to SEELE.

* * *

 **Lilith's Chamber, Old Geo-Front**

Evangelion Mark.06, or rather yet Leliel the 12th Angel of Adam, gave a growl as its shadow began alternating and shifting to form a large sphere larger than that of the previous Second Angel. All EVA pilots, aside from Kaworu, watched in horror as the shadow lifted to form an actual sphere just above Unit-13, comprised of sharp and small metal linings that enclosed the Mark.06.

"W-What the hell's going on?!" Asuka finally yelled with question.

"I'm thinking the Angel has grown some sort of mind of its own now that Lilith's death." Mari suggested, watching from above as the mark.06 was released from Leliel's captivity, monotonous and lifeless as it was lowered steadily to the bloodied ground. In an instant Leliel descended, with Unit-13 now enveloped by its form. Unit-02 quickly rushed forward, barrel whirling with Asuka growling. "Princess, don't bother, we don't even know what might come out!"

"Dammnit, Four-Eyes what other choice do we have?!" Asuka snapped back, raising her mini gun as it revved to life and firing with a battle cry. Leliel gave a shriek as its metal dispersed to form a gigantic Angel Core. "Damn, your right it's no use."

"I tried to tell you." Mari replied sheepishly, looking away from her scope. "Besides, I don't think Gendo planned this part out anyhow."

The Mark.09 watched as well not far as the Core began mutating, as is forming some sort of face or object. "Is that…" Rei Q watched with fear as the Core for a brief moment formed her own face with a twisted smile and evil giggle, making her shiver with fear. "Me? What… What am I?"

Inside Unit-13, Shinji continuously pulled at the controls of their Evangelion. Nothing was working, it was as it the connection with Unit-13 and the Angel caused some sort of energy discharge. "What the hell?! Why… Won't….. You…. Move?!" Shinji grunted, pulling at the controls with dreaded fear. "It's not responding, what's wrong with it?!"

Outside Unit-13's shoulder pylons burst apart, now seemingly replaced with dark marron stone like replacements that slowly built up. "Kaworu?" Shinji finally turned to his friend, fearful of what was happening. Everything was falling apart, and like a fool he didn't bother to question Kaworu if what he was doing really was right or wrong. "What's the hell's wrong with you?! Your acting like you just watched someone die!"

Kaworu didn't respond, how could he? Everything he'd hoped to give Shinji was now falling apart because of this unknown move played by the bastard Ikari. "How could I have been so blind? To think that I, the soul of the First Angel Adam so easily beaten by the Leliel the Twelfth," He murmured with sadness, looking up with lost hope. "I'm such a letdown…."

"What? _Your_ another Angel?! Wha.. How, what did my father do?!"

"It should have been so clear to me that the beginning and end are all but the same, and all easily devised by your bastard father Gendo Ikari…." He murmured, now fearful of how his scenario would play out. Shinji felt fear once more come up, Gendo had planned all this from the get-go? Had he known Shinji and Kaworu would attempt to use Unit-13 to steal the spears?! If so, how?!

Unit-13's eyes pulsed eyes as its mouth bolts finally gave way, releasing a roar of fury as it looked to the heavens it would drag down. The Core surround it had all but formed that of a large embryo, quickly shrinking to reform an Angel Core right before Unit-13's open mouth.

And that's when it happened.

That's when Shinji heard it. Or better yet, _him_ again.

" _Shinji, I won't let them take you away again….!"_

Unit-13's eyes suddenly pulsed white with a loud roar, blinding everyone in the chamber.

"What the hell?!" Asuka gasped, squinting her eye as her and others looked to see what was happening. The light slowly faded to reveal Unit-13's eyes now pulsed sky blue with its mouth closed. In an instant, Unit-13 slammed it head forward, sending the Core flying into the ground with a ground shaking quake. "What in the hells going on…?"

"it isn't awakened, so what is this?" Mari questioned as well. She hadn't seen what the Berserk mode was for Unit-01, so maybe this was similar to it? "Strange…. Might be the Berserk or….?"

" _Unit-02 and Unit-08, we have Akrid moving towards the opening, finish off Unit-13 and get here now!"_ Cap. Katsuragi's voice snapped, making Asuka flinch out of her trance. _"Unit-02, respond!"_

"U-Understood, we're heading up." Asuka called out, turning as Unit-13 began snarling and shaking as if struggling in pain. The concrete like stone pylons were ripped out as Leliel's shadow and the pylons reformed into the 12th Angel, with Unit-13 giving a cry of pain. The Angel growled as linings of white came across its form, before shifting to a single snake like body and quickly rushing out the ceiling opening with a shriek. "Damn, the Angel's gone! We'll have to deal with it later…. Four-Eyes we're leaving, we've got incoming Akrid! Let's get the hell out of here!"

"You got it!" Unit-08 began standing up, placing its sniper aside before firing a grapple down to the surface. Unit-02 jumped towards the grapple, quickly taking it and ascending as Unit-13 began lowering to the ground. "See you around, Puppy Boy…."

Rei Q watched silently, unsure of what to do now. The scenario the Commander originally designed was no broken, and they had no means to pull out the Black Moon. _What am I do be ordered to do now? Will I be destroyed for the next Ayanami clone to be reproduced?_ She questioned mentally with concern, looking from where Leliel had escaped to the larger Evangelion beside the Mark.06. S _hould I... Follow them...?_

Unit-13 slowly lowered till it was beside the Mark.06, slamming a spear into the ground. Shinji was so confused by this. "What in the hell is going….?" He murmured, unsure of what was occurring. All of a sudden, a halo pulsed to life above the Evangelion's head. "Huh?"

Unit-13 grabbed the Mark.06 as it lifted up into the air. All of a sudden, message appeared either Plug. _It's time we leave_ , it read as Unit-13 began rising faster. _Time to go home._

"Home….?" Shinji asked, though he didn't receive a response as the LCL pressure was sudden raised harshly. Shinji cried in pain as gasped one last time before he feel unconscious. "K….Kaworu…."

Said Fifth Child was watching Unit-13 with more so confusion than Shinji. At no point had he knew of Unit-13 being a Vessel of Adam up until the 12th Angels attempted union with its inner frame as he'd only assumed that Leliel desired a assimilation with himself and the EVA to cause another impact. But this… This was completely different than before, especially as to how Leliel left the Mark.06 without destroying its original frame. "What… Is this….?" He murmured, before he felt a massive heat wave come up around his neck. The 13th Angel gasped and tugged at his collar, unable to look to see the choker began disintegrating. "The… The choker it's….!"

 _You are friend of Shinji?_ Another message now read on Kaworu's screen, before it was replaced by another. _You, Angel or not, will live. Think this as token of gratitude for being there for Shinji when I could not be._

"Who are you? You cannot be the soul residing in Unit-01 nor an Ayanami clone. Who are you?"

 _I? I am no close of mother or Ayanami Rei. I am the Sixth Child._ The next message stated, before it was replaced with a silhouette of a person. Whoever they were had somewhat long hair with a soft, friendly smile and sky blue eyes which glowed and showed gratitude and recognition towards Kaworu.

" _I'm Shiro, Shiro Ikari. It's a pleasure to meet you."_

* * *

 **Surface, Old Tokyo-3**

On the surface, things were looking bleak as explosions, missiles and every sort of weapon went off all across the surface by New NERV HQ. WILLE's Wunder fired its array of cannons alongside its hovering fleet, hovering not far from the large inverted pyramid. "Ma'am, we've got multiple Akrid enclosing around the metal shaft! They're entering the inner parts of the Geo-Front!" Kitakami reported.

"Patter Yellow confirmed across all levels; they're all either Cat-L, S' or M." Aoba called.

"Any word on Units 02 and 08?" Cap. Katsuragi asked, looking to the Vice-Captain.

"The Akrid are for the most filling any space for exit," Ritsuko explained, pulling up a side image of New NERV and the Wunder beside it. "They'll have to go up the main shaft and find a way out NERV from there."

"Damn, and we're already in enemy territory as it it…" Katsuragi muttered. She didn't like this, how even with NERV and WILLE at each other's necks, they along with NEVEC willingly put most their differences aside for this common enemy. Still, she was happy to have at least one side with EVA's, even if they didn't follow their own standards or beliefs. "And Unit-13 and BM-03? What's their statuses?"

" _We had to take off before the Akrid got in."_ Asuka's radio spoke out with a hint of ignorance as the image of New NERV showed two moving dots, one labeled 'Unit-02D' and the other 'Unit-08.' _"Best guess is they've probably been eaten alive of captured for Thermal Energy in Unit-13."_

"Well that kills two birds with one stone," Ritsuko encouraged, looking over to Nagara. "Bring us closer to New NERV, have the left wing a 2 miles from the surface so our EVA's can get aboard."

"Roger," Nagara responded, pulling the controls slightly upwards. In an instant, Wunder began gently lowering, now close as possibly to the main shafts connection to New NERV.

A sudden alarm blared out, and Kitakami looked on the sonar to see several objects moving rapidly. "Captain Katsuragi ma'am, I'm picking up a large object moving rapidly towards us. It's definitely NEVEC!" She cried out.

"So they've finally shown themselves…. Bring our systems to Battle Station level 3! We cannot allow NEVEC to gain any ground here!" NEVEC, the word rang loud through the UN and what remained of the US government. A US supported faction dedicated to reforming peace in both major powers by using EVA and Thermal Energy to stop the Angel, Akrid and NERV crisis. Katsuragi remembered it differently though. She remembered a time where both they and NEVEC didn't exist, a time where it was all of them against NERV and SEELE before _then_ , and even close to being called family before the split of the two groups.

 _Had it not been for that damn Ikari, we'd have won this war ages ago_ , she thought with exasperate memories. _I'm sorry it had to end the way it did then, Shiro. Hopefully this will all work out in the end, and hopefully no one else deaths will be in vain…_

* * *

Not far off a large vessel moved rapidly towards the Akrid swamped zone. The object was a large hovering vessel built similar to a boat with a large tower like observation station above the main body, with the lower belly housing a large circular cargo station to the read with a curved command bridge in front of it. Above the bridge was a thin wing like deck which connected to the far back and ended with two prongs far out from the bridge end. Finally the ship was topped off with two large thruster engines underneath the thin like deck on either side, with smaller engines on the center body.

It wasn't a big as the Wunder, though it packed serious firepower as it had two large double barrel artillery cannons on either side of the hull with smaller cannons scattered across the front, sides and back. Finally on the wing deck were the word 'US NEVEC STORMBREAKER' in English and Japanese on either side.

The large cargo bay began flashing several lights across the outer hull as the large panels began opening. In that small moment, the Stormbreaker rushed forward till it was just above the Akrid. Instantaneously, the twin cannons turned downwards and fired large explosive rounds to the surface. Akrid and dirt were sent flying in all directions, with flying Akrid rushing towards the sky. The panel opened and out rushed to objects.

The first was a red and blue colored Evangelion, built in similar design to the original Unit-05 though with reinforced and re-armored legs and now humanoid EVA arms. The other was dinosaur in appearance, designed with a more militaristic look than the normal humanoid or organic design of EVA. It had two large Anti-Akrid cannons on the top close to the legs connection to the main body, which had raptor like arms with sharp claws, finally topped off with a slanted tip pointed head.

"This is Trident, Operation Renewal is a go!" The pilot of this military mecha, codenamed the Trident Land Cruiser or TRIDENT for short, was Mana Kirishima. She was young for a pilot of her age, with short brown hair and bluebell eyes, thought it wasn't anything to concerning as WILLE and NERV had already done before and after Near-Third Impact. She wore desert sand colored armor on her gloves and chest atop a dark blue sleeveless jumpsuit. The armor covered her shoulders and half of her torso, with a small red crystal outlined by a silver circle with the word 'NEVEC' on her left shoulder. "We're moving in! Musashi, how are you holding up?"

"Good so far, glad to see the design frame of Unit-05 still works, even if it was just a body with sticks for legs!" The pilot of the Unit-05 rebuild, now EVA Unit-07, was Mana's friend Musashi Lee Strasberg. He like Mana wore the exact same armor, though he kept on his helmet as Mana didn't. He had dark purple hair similar to Katsuragi's hair color, though shortened to being above his neck with dark green eyes.

 _"This is Lt. Colonel Geno Suveraji on all NEVEC channels. Operation Renewal has been approved. EVA Wolfpac and EVA EURO Heurtebize are still under weapon finalization, so you'll have be on your own for the beginning duration of the Operation. Unit-TRIDENT, move in to secure the objective. Unit-07, defend the opening so SI and Trident can escape. TRIDENT, move in and secure SI before returning back to the surface!"_

"Understood," Mana replied, pulling the controls as her Tridents feet began lighting up. On the bottom soles of the feet were engines with smaller one on the back framing. "Engines now are active!"

Trident rushed forward into the hole made by the earlier explosion as Unit-05 landed close to the hole. "You get going, Mana! I'll hold these bastards off." Musashi called out, pulling up Unit-07's jousting lance and the built on Pallet Rifle on its right hand. Akrid began finally returning from the explosive area, growling and snarling as they began rushing forward. "Out the fire and into the frying pan indeed…."

* * *

 _ **A/N: I think I have too many ideas for my own good. I won't lie when I say I've written almost 4 versions of this chapter before finally settling with this one. Anyways, I've finally started the transition from the 3.3 ending to the new one. I hope to make it enjoyable for you all, so please do wait for when the next comes out. I should also mention, the NEVEC Stormbreaker is based off a spaceship art I've had for a while.**_

 _ **Here is the link:**_

 _ **That said, this is the KnightOfZ3R0 signing off!**_


	10. Chapter 10

_**A/N: I apologize deeply for the late update on the story, I've had a lot of projects my teacher are having us do all of a sudden(Because apparently we "didn't have any time" for any of this career project crap in school), and I've been getting a lot of inspiration for writing another Code Geass story (This time I actually know what I'm writing unlike the first time). Though that shall wait as I plan on completing this one first.**_

 _ **Neon Genesis Evangelion, the End of Evangelion, and the Rebuild of Evangelion are owned by Hideaki Anno and written by Yoshiyuki Sadamoto. I own no elements from the original Manga, TV show, or Rebuild and EOE films but my OC's.**_

 _ **That said, Please Enjoy The Show!**_

Talking-"Hello"  
Radio/EVA Voice-" _Hello_ "  
Thoughts- _Hello_  
VEELE/VEELE Clones-" _ **Hello**_ "  
A.I-" **Hello** "

* * *

 **Chapter 10: NEVEC**

 **NEVEC Stormbreaker, Old Tokyo-3**

The command center of Stormbreaker was large for normal command deck standard, with a center command platform surrounded by several floor all connecting to the sides of the bridge or front glass frame. Multiple men and women rushed by or spoke rapidly, with the emergency alarms finally shutting down to give some silence. "What's our status on…?"

" _Cat-L Akrid moving to western sector!"_

"Unit-05 had dealt with the third Chryatis Cat-G…."

"Main cannons now reloading!"

" _Shields holding, all remaining Anti-Akrid cannons fire at the…."_

"Wolfpac configuration now at 80% completion!"

"And EURO Heurtebiza?" Aboard the Stormbreaker's command platform stood a man in his mid-twenties. He had black hair with lime green eyes, wearing a tight black long sleeve with black and white cargo pants. On his beast pocket was the word 'NEVEC' with the insignia above it. The logo was designed like an X with its top lines having three lings connected out with a small diamond above the logo. "How's Anno's EVA coming along?"

" _We'll have it done in 10 minutes tops, five if we rush the Air System here as soon as possible!"_ A voice called through the comm link.

"Copy, report in when you're done."

" _You got it, Col." Let's hope we can last out that long,_ Geno Suveraji thought to himself. _If we lose this position, we'll be sitting ducks for that damn Cat-G we lost getting here, or worse the other Akrid that hit NEOS… Hopefully it can't find us-_

"Colonel, we've got incoming!" The large glass front windows magnified in form, locking onto a plethora of objects moving forward. They weren't much to see; similar to the body of a scorpion, they processed two large scorpion like tails for arms with large four claws as their ends, with legs now replaced by pale white wings. He head was nowhere to be seen, as the main body had tough skin across its usually open to see black eyes. "Akrid, Cat-L's; Moythric type!"

"Damn, bring all front cannons to full power!" Geno issued, with the center platform descending to the second floor. Geno easily marched to the closet radar technicians station, looking with the worker as multiple clusters of red dots began converging towards the Stormbreaker's center dot. "Son of a bitch, these Akrid are clever aren't they? Watch all sides of the ship, knowing them they'll be aiming for our Thermal Energy supply tanks!"

"Yes sir."

"Understood, sir!"

"Jerald, you'd better have Heurtebiza up and running in a few seconds, at best." Geno warned into his collar comm. No response, which only helped to worsen Geno's annoyance. "Jerald!"

" _You can't rush life or death killing machine production, Gen. You know that~!"_

"Oh yes I sure as hell can!"

" _This is EVA-US Wolfpac, I'm done and heading out!"_ Another voice called out through the ships main communication channels.

"Solid copy, Sorani. Give them hell, and help defend that damn hole!" Geno reinforced, before moving away from the radar techs station. Outside the bridge, small and large bullets and explosions ripped apart the slowly darkening blue sky, with Stormbreaker and Wunder firing on all direction. At the underbelly of the Stormbreaker, a large object rushed out from its opening. This object was a rather large machine, dwarfing the size of the common Evangelion as it was designed feline almost, like that of a wolf and cat combination.

It was for the most silver colored with five sharp claws on all paws with the main body covered by wolf like fur. Small armor pieces covered the main body was well as the seemingly organic and metal fused legs, with a metal tail at the back with a sharp point. Finally its head, which was cat like in designed with sharp EVA designed teeth and jaw, connected to its back where the Entry Plug cover sat next to 2 pairs of EVA restriction energy cells on either side. On the side of the left hind leg was the NEVEC symbol, with the words 'US WOLFPAC' on either hind legs ankle sides.

The Wolfpac roared loudly as it crashed down into the surface, looking towards the occupation before it. The Akrid weren't much luckily against Sorani's EVA, mostly just Ermmild, GoreVorgg, and Tangaant. The Tangaant were scorpion in designer, with six legs, a large tail with a poisonous tip and large skin armor at its font with glowing blue wavers on it. Underneath the 'head' was a pair of arms ending with sharp points like the tail as well.

The Ermmild were probably the weakest of the group, slug like with an arrow like head connected to its inner body, which was surrounded by skin armor like most Akrid. Though they were slow, they packed a punch a times and were half the size of Wolfpac and normal Akrid.

Then there was the GoreVorgg, which seemed like a fusion of a crab and rhino. With stone colored skin it processed a large crap like left arm and a deformed right arm at the front, close to protect its mutated rhino like face, which was already covered by armor spikes and a twisted mouth. Connected to its head was a large back seeming almost like ripped apart snail shell, connected to its five unarmored legs in a spider like formation.

"Damn this might be tougher than I thought," inside Wolfpac's Entry Plug, another young woman sat inside, hands gripping the controls tightly in deep thought. Well, not really young as she was close to 20, but still considered young in the NEVEC command line. She had short red hair which ended just below her neck and slowly turned bright blue at the end, with green eyes to match her NEVEC pilot suit. "Hopefully this doesn't end too badly…."

Wolfpac roared violently before it jumped high and fast into the occupation, tearing right though any Akrid unfortunate to get in its way. The Ermmild and Tangaant were pathetically simply to bypass, it was the GoreVorgg that stood as the 'guardian' of the opening. It rushed forward with alarming speed, screeching as it rammed into Wolfpac's legs. The EVA hybrid dodged to the side, turning around in time to latch its teeth onto one of the GoreVorgg's legs.

The GoreVorgg in response ran in all directions, ripping past its Akrid siblings to get the giant off of it. Finally it did as it rammed head first into one of the old structures that remained after THN, sending Wolfpac flying only closer to its goal. "Musashi, how ae you holding up?"

"Could be a lot more, ngh a lot more better!" Unit-07 jumped and dodged seemingly everything, firing its wrist rifle and cutting past anything trying to get in. "If only WILLE was willing to let their EVA's come down and fight, not leave us to do their damn dirty work!"

" _Yeah, that'll probably never happen with Katsuragi in control,"_ came the reply.

" _Oh calm down you two,"_ Mana's voice replied though the comms. _"It's not that bad!"_

"Yeah, not bad for you Mana! Considering you're _below_ this giant battle going on!"

" _Touché."_

"Yeah… Speaking of which, how's it going down there huh?" Musashi asked as Unit-07 jumped into the air once more.

" _Good so far, managed to find SI, along with some interesting new EVA's we'll be having on the team,"_ Mana replied, somewhat hesitantly before muttering to herself. _"Man, Mk.-06 and Mark.-09 on our side with Unit-13 as backup? This day just got a whole lot better!"_

" _Too all forces in the area, we have a high speed object moving through the airspace,"_ this communication can from, surprisingly, Wunder's Vice-Captain Ritsuko. _"MAGI confirms it's an Akrid."_

" _Must be that damn thing that tore through NEOS earlier then!"_ Sorani snapped, her Wolfpac finally making the high jump and landing close to Unit-07 and the entry point, sending Akrid and old wreckage flying. _"Where is it? Where is that thi-AGH!"_

Wolfpac was suddenly sent flying into the large opening as said Akrid crashed with an explosive wave of energy. The wave burned apart any unfortunate Akrid, though Unit-07 was luckily saved by its booster systems on its legs. In the center of the implosion was a large creature at least twice the size of the Wolfpac, with large wings that seemingly frightened any other Akrid in the area. "What the hell, the Akrid are… retreating?" Musashi uttered in confusion, and slight fear as he looked towards this new Akrid.

It was dragon like, with long spikes going down its neck all the way to its long tail, ending with 3 spikes on either side on the tail end. Its front legs were long, with ankles ending with hoof like stubs and sharp curving spikes close to the knee parts close to the upper arm like area of its body. Its legs were velociraptor, though shorter than the larger legs with stub endings as well. Finally there was the head, with a large horn above three pairs of red eyes. Its neck was long and like its body had spikes atop the neck, connected to the head which already had 4 long spikes, two on either side of the head and another lower two pointing slightly downwards.

The creature's eyes pulsed, before it let its mouth loose with a twisted scream. The lower jaw split into 4 tendrils as it roared, with the lower half of the neck splitting apart to reveal 6 arm like sharp claws that waved in the air. "Son of a bitch, it's huge!" Musashi yelled out, rushing back as the unidentified Akrid looked towards his EVA. His Unit-07 barely made it away as one of the creatures stubs slammed into the ground, sending his EVA flying into the air. "Augh!"

" _Musashi? Musashi, Sorani respond!"_ Mana cried out over the comms, Musashi was already unconscious from the harsh blow done by the Akrid.

* * *

 **Lilith's Chamber, Old Geo-Front**

"Damnit," Mana groaned, slamming her fist into the all of the Entry Plug with fear and anger. They hadn't anticipated the Akrid being able to find them, but it was clear the thing was a loose cannon and well known by the other Akrid. _Something able to send Akrid running in terror?_ Mana thought back to Musashi's last transmission with concern. _That's not good, especially if it's an Akrid or Angel and not a human weapon…_

Unit-13 and Mark.09, meanwhile, stood on guard surrounded by GoreVorgg corpses as Kaworu continuously tried reactivating the Mark.06. After Unit-13's soul was revealed, Kaworu immediately got to the task of trying to bring the Mark.06 back online. He'd only managed to get the Entry Plug systems active and the outer camera feeds online, but not the EVA itself unfortunately.

As for Mana, she'd gotten into the chamber just as Unit's 02 and 08 entered the tunnel leading up to New NERV HQ. They'd been there for almost a good 15 minutes at best before Unit-13's mouth sudden opened _"Forget… Mark.06."_ The voice that came out was robotic yet somewhat human and loose with its wording, though it was still understandable for the most. _"Must… ascend to Storm…. Will take Mark.06 as well…."_

"I agree, we've wasted enough time unfortunately." Kaworu concurred, the Entry Plug of Mk.06 escaping the neck as the Fifth Child exited and looked to the group of large machines. "Leliel has managed to completely wreck the inner systems of this EVA, so we will have to rebuild it if we are to have it on the battlefield once more.

"Alright then," Mana had TRIDENT quickly turned towards the Unit-13 and the Mk.09 in question, though Mark.09 was the only one that looked to the larger mecha. "Which one of you will take this thing home then?"

" _I will…."_ Unit-13 stated, its inner armed once more extending as the giant walked towards the downed Mark.06. Kaworu quickly moved back into his previous EVA's Entry Plug as Unit-13 pulled it up, adjusting the predecessor close to its shoulder pylon. _"Have more speed and RS Hoppers…. More powerful defense…."_

"Alright then, guess we got a plan." Mana replied, looking to the Mark.09 with hesitance. While it was true she liked having more Evangelions on their side, that didn't necessarily make the Mark.09 a good guy. But still, Gendo had clearly had her for a means to an end, so she really didn't have anywhere or anyone else to go to but NEVEC or WILLE. "Mark.09 pilot, you and I will provide support if Unit-13's RS Hoppers go south, so keep that scythe of yours at the ready!"

"Understood." Rei Q replied, fixed the Entry Plug's internal system. While she did have major control of her EVA, the head and outer camera feeds were slightly damaged during the skirmish before. "I will try my best to keep up."

"Good," Mana quickly switched communications, more specifically the Stormbreaker's visual comm link. "Stormbreaker, this is TRI-01. We're heading back up, over."

" _Acknowledged, be careful heading here Mana. We're facing an unidentified Akrid."_ Suveraji replied, turning away as the NEVEC cruiser shook violently with an Akrid screech and explosion sounds in the background. _"Get the A.T Field active, immediately! And have_ _EURO Heurtebiza begin covering support with the southern wing!"_

"Understood." TRIDENT's thrusters quickly kicked back to life as Unit-13's second pair of RS Hoppers came to life and rushed into the sky, tearing at anything that could slow the group down. As Unit-13 quickly began climbing upwards, TRIDENT glanced to Mark.09 and a Spear of Longinus not far from its position. "Hey, Mark.09? Bring one of the Spears with us, will ya? Might need it when we meet up with that Akrid up top!"

" _Yes, Ma'am."_ Mark.09 steadily walked towards the Spear, taking the red spiraling lance up before jumping upwards. Almost with ease, the Mark.09 began cutting into the wall and climbing upwards. TRIDENT quickly followed suite, firing rounds and missiles into the walls to force the opening larger than before.

The more closer they got back to the surface, the more communications began yelling and screaming, which only fed more concern to Mana. The Akrid had managed to rip right through NEOS, which was already reinforced multiple times for obvious reasons. And yet it didn't bother to stop and simply burn the space base, far from it the Akrid tried to follow them back into the Pacific Ocean with that damn Red-Eye Akrid….

 _Just what the hell is going on?_ The redhead thought silently, glaring upwards to the light that escaped from the far opening. _All this happens just as we get SI back from NERV, and Unit-01 returns from stasis… And with not Fourth Impact activating you'd think the Akrid would settle with what remaining Thermal Energy there was…. Unless the Akrid are somehow all connected to this specific Akrid or realize something is going on that we don't know about…._

* * *

"Alright, how do you like this?!" Musashi screamed in rage, throwing his Lance right into the Akrid's waving neck. The demon creature roared as orange liquid began spewing out like blood, its eyes darting before it jumped high into the air. Its front legs began suddenly glowing white and before Unit-07 could jump as well, its feet slammed cruelly into the ground. "Son of a bitch, a shockwave attack?!"

The already unstable ground exploded and send Unit-07 back, but the blue Evangelion's pilot was not willing to go down so easily, not when they were this close! The Akrid roared as its wings spread out, ready to pounce onto its target. Before it could even begin flying, Wolfpac once more jumped into the fray. "I won't let your freak race take anyone else!" Sorani yelled out, pushing her EVA hybrids controls beyond before as the giant animal rushed onto the Akrid.

The Akrid and Wolfpac seemingly fell into a dog vs dog fight, though with Wolfpac's speed it was relatively hard for the giant creature to grab it. All of a sudden another spear, this time a blade like cross connecting to a silver staff ripped right through the neck of the Akrid and into one of the wings of the creature.

"Sorry I'm late, had to deal with those damn flying Akrid earlier." That voice came from upwards, revealing an Evangelion similarly designed to WILLE's Unit-02. The humanoid was completely light grey, with the main chest and torso similar to the concept behind the Unit-04 from old NERV US, though with the NEVEC logo implanted onto the center piece. Its shoulder pylons also remained, though with an inner red design on them and with a more curved layout. The head also retained Unit-02'd design, though light grey to match the armor color and red eyes, the only real difference in visual design was the forehead was smoothed out unlike Unit-02's original orange crescent piece.

Though this EVA, unlike most before it, was gifted with flight thanks to NEVEC's flight system. The system was a pair of short curving wings connected by a large back piece and onto the EVA's center back area. On either wing were vent like openings with two large propeller like thrusters on either side. This EVA was NEVEC's EVA EURO Heurtebize, the only known EVA so far able to fly.

"Ugh, goddamn it V-02 always late as ever!" Sorani growled, jumping onto the Akrid's secondary wing as Heurtebize charged forward. It easily spun and landed a harsh kick to the Akrid's face, ripping apart its crown like armor to expose its inner orange skin. "Just how many times are you going to be late, huh?"

"Be grateful I was even able to fly here, I could be back at home just chilling and drinking coffee as usual," the pilot of Heurtebize was a young man with silver eyes and white hair, wearing a silver and chrome EVA Plugsuit with small tubed connected underneath its armpits, the forearms and shoulder blades. "This thing, Akrid X, it's the one from space right?"

"Really? Akrid X, that's the best name command came up with?" Musashi asked as his Unit-07 began raining back bullets onto the giant.

"Oh they didn't make it, I did!" V-02 replied sheepishly, before his EVA gave a whirl of fury as it rushed forward. "Hey Sor, jump!"

Wolfpac quickly jumped at the EURO EVA slammed its feet into Akrid X, the neck giving a twisted loud snap at the monster was sent flying. Sorani shivered and twitched at the noise, groaning loudly as she covered her ears "God I hate that noise!" She cried, before her EVA was suddenly tugged backwards. "Huh?"

The NEVEC pilot looked to see TRIDENT now holding onto her EVA by its metal jaw, rushing upwards with Unit-13 now close behind. "Mana?! The heck are you doing, the Akrid is back that way!"

"All EVA forces, return to Stormbreaker immediately." Colonel Geno's voice suddenly came up across the many communication lines. "Command's calling for an immediate recall. We're pulling out!"

"Roger." Heurtebize's engines flared to life loudly, and with little to no haste as it quickly took it and Unit-07's lance and spear, before rushing by the Mark.09 and taking it up. Rei Q's EVA showed surprise but it was quickly blocked out by V-02's voice. "Don't worry, I got you!"

"R…Right…" _That voice_ , Rei Q thought to herself. _It's so… familiar and so…_

* * *

 _"This is… Shiro Ikari, NEVEC Stormbreaker Commander and pilot of Unit-13…. I'm ordering full withdraw back to NEVEC Headquarters immediately, Geno. On the double!"_

"Yes sir!" Suveragi's reply came, and with an extra message at the end. "And Shiro…. It's good to have you back…. You know?"

Inside Unit-13's secondary Entry Plug was now a figure, with short cut hair and sky blue eyes smiled. He wore an old NERV EVA Plugsuit, with a leather jacket with the NERV US logo and NEVEC insignia on its front. He was Shiro Ikari, brother of Shinji and second in command of NEVEC. _"Good to be back."_

Shiro laid back slightly, sighing in relief as he looked to his brother who laid safely asleep in the other Entry Plug. _"Shinji, brother…"_ the Ex-Sixth Child uttered, placing a hand to the Plug's side as his eyes began watering. _"You're alive…. I'm so happy…."_

* * *

 _ **A/N: I should say that the WOLFPAC and HEURTEBIZE are actual Evangelion's you can find on the internet, and though they were not used in the series or Rebuild I figured it was nice to show other EVA's aside from the original cast of humanoid machines.**_

 _ **That said, this is the KnightOfZ3R0 signing off!**_


	11. Chapter 11

_**A/N: FINALLY, IT'S OVER ITS DONE! NO MORE GODDAMN SCHOOL FOR THE NEXT TWO MONTHS! YES! YES! Well, now that I got that out of my system, I deeply apologize for the very much late update. I had a lot of garbage final "exams" to do, (swear some of these teachers weren't even trying to pass us.) which took up a lot of my time as my teachers wanted me to do those "Exam" projects**_ **outside** _ **of school with my friends who don't know where the hell any of us live at. But yeah, so that was fun and all… But now I'm back, and hopefully I'll be able to finish this story for you all!**_

 _ **Neon Genesis Evangelion, the End of Evangelion, and the Rebuild of Evangelion are owned by Hideaki Anno and written by Yoshiyuki Sadamoto. I own no elements from the original Manga, TV show, or Rebuild and EOE films but my OC's.**_

 _ **That said, Please Enjoy The Show!**_

* * *

 **Chapter 11: Plans**

 **New NERV HQ, old Tokyo-03**

Just above the newly made crater above Lilith's chamber sat several hundreds of Akrid rushing the opening. Whilst most moved to crawl in towards the massive skeleton site, none bothered to notice the larger object just between the chamber and surface plating. A large vessel laid, one just twice the size of WILLE's Wunder where a lone pair awaited. "It appears the Third and Fifth Child were unable to lift the Black Moon as you predicted, Ikari." Prof. Fuyutsuki stated softly, looking down as the many Akrid forms descended into Lilith's old chamber.

He and Ikari now moved to a large sphere like chamber, completely black with red linings across the inner walls. Fuyutsuki himself stood on a small separate platform looking through the spheres walls, while Ikari sat in the center in thought.

 _Funny enough, out of everything he could have brought, he brought his desk to think upon._ Fuyutsuki silently thought with a small smile. _Ironic I guess… The only real friend Ikari has really had was that damn desk of his, just as silent and emotionless as himself…._

"No, the Black Moon would have been brought out had I not dismissed Unit-13's Soul awakening." Ikari said calmly, fixing looking down at Key to Nebuchadnezzar. Or rather, what remains of Key to Nebuchadnezzar. The human nervous system design seemingly disappeared from the yellow glass frame, though the glass was cracked, allowing the larger end piece like key to move separately. "Though I did not predict Shiro would be able to speak through Unit-13, nor control it like a human body."

"Do you think his human body and Unit-13's body are becoming one in the same?"

"Possibly… Though if this were the case then it's likely to assume Shiro's physical body is becoming that of an Evangelion."

"Is that even possible….?" Even Fuyutsuki had to admit, an EVA the size of a human sounded impossible. Though from all the things that had occurred over the past few years after Near-Third Impact, it wasn't too out there… "Ikari…."

"I... Admit I do not know. But if this is the case, then it's possible…." _It's possible Yui might be able to possess a body earlier than anticipated should we get to Unit-01 before NEVEC_ , he thought to himself. _Maybe even… No. It wouldn't be perfect enough. For Yui, her body must be perfect and absolute! Although now that we know this… Hmm, Shiro you simple minded experiment…. You've given me another clue to the true secrets of Evangelions soul._

"All that matters is the recapturing of Shinji Ikari and Rei Q as well as possibly regaining control over EVA Units 01 and 13." He stated, calmly moving his hand onto the desk. The desk hummed to life, revealing a holographic display showing several screens and designs. The ones Ikari focused on most of all, however, were the Mass-Produced Evangelion that were finished and finalized for combat, a file labeled "V.K-S.I genetic finalization," and SCC _Sairentodamu_. "We'll have all forces move around the perimeter of _Sairentodamu_ , and prepare all cloning facilities before WILLE or NEVEC return to find us."

"And the SEELE-Type EVA Models? What of those?"

"…" Ikari went silent, a frown upon his face which somewhat worried Fuyutsuki.

"Ikari?"

"….Have them ready in the event we fail to pull out the Black Moon…. They shall be our final resort…."

* * *

 **WILLE, AAA Wunder 3 kilometers passing over old India**

"It is confirmed that Ex-NERV Third Child Shinji Ikari has been taken by US Forces NEVEC along with NERV's newest model, Evangelion Unit-13." Captain Katsuragi found herself sitting at a half cut circular desk with several holographic videos across the desk. On the feeds were several men and women, each with several small logos of European countries in the bottom corners.

" _And the core of Unit-13?"_ One of the European speakers, more specifically for the UK, spoke up with clear extreme concern. _"Our knowledge states the EVA managed to awaken before it was abruptly brought out of its awakened state."_

"Yes, well to our own knowledge sir," Katsuragi spoke up once more, fixing one of her bangs as she looked to her side. "We really don't have any prior or present knowledge of how this was possible. Vice-Captain Akagi believes that the soul of EVA 13 was somehow able to purge the Angel, codenamed Leliel, and escaped with NERV and NEVEC's EVA squad as well as the newly uncovered EVA Mk.06 into the US."

" _I see."_

" _Captain Katsuragi if I may?"_ Another member, this one acting as Germany's speaker, called the WILLE commander out with little haste. _"As you already know NERV Germany, or rather WILLE Germany, is still able to get through small breaches into the old MAGI System. We have reason to believe that Ikari has attempted to raise the Black Moon from underneath Tokyo-03 in old Japan, but with Unit-13 now in NEVEC's possession that renders him without a strong enough EVA to raise the Moon out."_

" _That said, it's not out of the loop to assume Ikari has multiple Mass-Produced Evangelion construction facilities near New NERV's Tower of Babel. And whilst WILLE has the stolen SEELE's primary transport and warship with several Evangelion's protecting her and her crew, we still do not know of how many hidden forces or Mass-Produced EVA's lurk under Ikari and SEELE's command. As much as it pains me to say this, once more have little to no choice; we may need to request an alliance with the US and WILLE once more."_

The speaker was unable to even get the sentence out before another speaker from Spain laughed at him. _"An alliance with NEVEC? Ha, you fool that's impossible!"_

" _Unfortunately I must agree,"_ A female speaker from Ukraine spoke out with sadness. _"This is indeed true. You all know, as well as myself that the last time we attempted an alliance with NEVEC and the US they went behind out backs, even going so far as to allow one of their commanders to die in old NERV after the reactor meltdown, even going so far as to launch Unit-01 into orbit!"_

" _Even if we could form an alliance with the US and NEVEC, neither their command nor government would allow us back into US territory….."_ An Indian speaker reinstated, though he clearly held hack what else he wished to say about NEVEC.

Katsuragi herself had to mentally bit her lip to refrain for speaking out. She knew the truth about what happened there, as did Shiro and the rest of NEVEC's EVA Force, and God could only do so much to shield Katsuragi if the UN was able to discover this. _It was for the best! Besides if I didn't do it, we would have lost everything and even more to NERV! And not just our home or Earth, but…._ She mentally reassured herself, though she gulped down her fear and finally responded. "Yes, unfortunately NEVEC is not in agreeing terms with us. We have no choice at the moment but to monitor New NERV and hope Ikari does not gain any more ground from where he is."

" _Yes, pray that he does not."_ The speaker from the UK answered back. _"Until we can come up with a solution, continue monitoring NERV movement as well as the unknown Akrid-X from the earlier skirmish. This meeting is over, you may all leave."_

And just like that, the speakers video feeds vanished, leaving Katsuragi alone in silence. Her mind threatened to have her eyes spill out tears of both joy and regret, but she forced it away. She'd save her tears for when she really needed them. As Katsuragi left her room, she noticed Asuka glaring at her. "You're kidding me?" She growled, pushing herself off the side of the wall. "We're going to form another alliance with those backstabbers? Even after everything they've done to us?!"

"Do you know of any other major forces that can help us?!" Katsuragi snapped harshly back, glaring under her sunglasses as the redhead. "If so, please tell me now!"

Asuka went silent, glaring away and muttering to herself.

"Look, as much as I myself hate this we have little choice…." Katsuragi explained, fixing her bangs as she spoke softly, though she still held a stern tone. "NEVEC has multiple warships, artificial intelligence's, and worst of all a lot more EVA's than us. We need their support, especially if we're going through with Plan 08+02."

"The idea to fuse Unit's 02 and 08 to create an EVA on par with NER- Sorry, _NEVEC's_ new toy Unit-13." Asuka hated the idea the moment the UN thought of it. That was it, nothing could be said or done to change her mind. Unit-02 was, by definition, Asuka's only true friend during the Angel-EVA Crisis and to lose half of it was on par with losing her mother once more. She valued Unit-02 more than anyone on the planet, even…. "Well you can forget it. Besides I sure as hell won't sign off on it, and you need my signature of approval to do it."

"Asuka, I get it okay? Unit-02 is the closest thing you have to-"

"No….No! No, Misato you don't get it alright?!" Asuka cut in, her eye narrowing with tears threatening to come out. "Unit-02 is the only real family I've had since Shinji…. Since then! If I lose my Unit-02, I'll have lost everything!"

"You don't think any of us have lost anything, Asuka?!" Katsuragi argued, her emotions finally coming out. "You think you're the only one who lost something they loved that day? Huh, is that what you think?!"

"Yeah, sometimes I do considering your still trying to put up that damn act!"

"What act?!"

"You know what, don't play fucking dumb with me Misato! Everyone knows your trying to play the 'Commander Ikari' act of WILLE!"

"I….." Katsuragi bit her lip; she hadn't any other words to say.

"Well when you finally stop trying to play Ikari, let me know and I might get back to you about Unit-02+08!" Asuka snapped, turning and rushing away, leaving Katsuragi alone in the hallway.

 _Stupid Shinji, Stupid Shinji, Stupid Shinji, Stupid Shinji!_ Asuka mentally screamed, gritting her teeth as she felt water ready to burst out her eye. "Damn it!" She finally screamed, slamming her fist into the wall before her breathing stuttered into slight sobs. "D-Damn it…. S-Stupid…. Fucking…. S-S-Shinji…!"

* * *

 **Meanwhile, US NEVEC Stormbreaker**

Shinji tossed somewhat in his newfound bed, his mind finally coming back to live. His eyes opened with blurriness before he rubbed them softly. _Another unfamiliar ceiling, just when does this train of déjà vu end?_ His mind thought out, before Shinji focusing on when he was.

"Hmmmm... What the….?" The old Third Child was only able to muster that out before his eyes focused on his newfound room. No longer was he in a hospital like at New NERV but rather a lite up medical chamber, with several medical devices and tools on the side of his bed. One the wall opposite of him was a door, next to it was a desk which spanned to the other end of the wall with a computer built onto it. On the right was a white curtain partial open to show another bed next to his, with another person laying under blankets. "What is this place….?"

"Oh, you're awake!" Shinji blinked and looked to see a male in a white doctor's jacket enter the room. He had a black hair wrapped in a ponytail, similar to Kaji's hairstyle only his hair was somewhat longer ending just blow his elbows. He also had a thin mustache and what looked like a bifocal on his right eye. "I'm sorry for the turbulence you've probably been feeling, traveling across the Pacific at high speeds is very… challenging for the human stomach."

"Traveling across the Pacific… wha-?" Suddenly Shinji felt his stomach give a hard jerk which made himself jerk forward. It felt like his previous food wanted to burst out, before it gently lowered back down his throat to where it belonged. "God, I hope that happen again…."

"Oh trust me, it will unfortunately though you don't have to worry about it coming out in any other ways." The doctor stated, before he took a black stethoscope out from the left wall and walked calmly over to Shinji. Shinji didn't even need to listen to what the doctor had to say before he started breathing in and out slowly at the older man check his pulse. "Hm… No heart differentiation from the sounds of it…"

* * *

 **Stormbreaker Command Deck**

" _While we are glad to see you have return from NERV, Commander Shiro we still hold concern regarding the Tower of Babel's MAGI Defense Systems,"_ At the moment NEVEC Commander Shiro Ikari stood before several curving screens which sat around him. On each one was a different person, each acting as spokesmen for the US Congress and NEVEC military command line _. "As well as the whereabouts of Akrid-X."_

"I assume you, with Unit-13's capture we will be able to slip by the defense grid, and even then the old MAGI system is in complete disarray." Shiro explained, fixing the collar of his jacket. "As For Akrid-X, we lost sight of it once we immediately left NERV HQ and WILLE's Wunder."

" _I see."_ A congressman stated, sighing in defeat. For almost 14 years, the Akrid race had been kept at bay from getting near Old Japan and New NERV after Near-Third Impact. Yet with the sudden uproar of Akrid sightings and this space Akrid, it showed signs of a possible invasion. _"Do you believe this has to do with the return of Evangelion Unit-01?"_

"A possibility as the EVA was believed to have been giving off massive Thermal Energy waves before and after retrieval. Though that remains to be seen till we can initiate the operation."

" _Your objective was the retrieval of EVA Unit-01 and possible deactivation of the Autonomous Assault Ark Wunder, correct?"_

"Yes. If we can ground the Wunder and take Unit-01 back sir, I feel we will have a higher knowledge of how these Akrid came to be. That and we will finally have a MAGI system we no longer have to hack, which may possibly have the files we need to figure out this mystery."

" _I see. Very well, continue monitoring for Akrid-X and any possible NERV movements. Meanwhile regarding the Wunder, we shall get back to you on the operation planning."_ The congressman stated, to which Shiro bowed before the screens all shut off. The Ex-Sixth Child sighed, turning around and making his leave towards the close door.

"Well that could have gone a lot better than I anticipated. Then again, the last I'd seen Congress or the President and his Wiseman's Committee was almost 3-4 years ago so maybe I should have changed and fixed myself." At the moment, Shiro looked like a mess, with his jacket and plug suit dirtied by age and his hair wild in appearance. His hair was spikier and stood out though, with several white strands of hair.

Being in an Evangelion was not as easy as he'd hoped so long ago, and it only got worse after he force purged the Leliel Angel out his EVA body frame. The only real difference was probably the fact he had his body back. His actual body, one that no longer had to rely on machines or prosthetics which was probably his only pro. "At least they still remember me! For now that is…." He uttered silently, fixing his Plugsuits collar.

Shiro looked around as he exited his small room, now faced before the main bridge. _God, to think this is Stormbreaker, and that is only a small blueprint right after NTI…._ He thought to himself, looking at the people who walked by or worked at their stations called out or speaking to one another. _To think this battleship was only a small fraction of an idea made by WILLE once now is our own device…. Guess I should thank…_ her _… for the idea._

The Ex-Sixth Child felt his heart tug at the mention of WILLE's commander, or rather captain as she went by. He hated her, with ever fiber in his body after what she'd done and said about Shinji. He sighed and dismissed the cruel memory, before he felt someone sharply jump onto him. "Oh God I'm being touched inappropriately, help!" he cried out, laughing as he heard the other laugh as well. "Why do I have a feeling that was your real goal, Mana?"

"Hey, I'm not like that! Most of the time, anyways….." Mana retorted, jumping off the EVA pilot and rushing in front of him. That is, before she gave him a jab in the shoulder. "Also, that's for making all of us wait so long!"

"Ahaha… I'm sorry, Mana I really am." Shiro replied softly, yet with a hint of nervousness at the end. "Had I known Katsuragi discovered how to do…. That…. Well that then…. Things would have gone differently…."

"Hey," Mana reassured, placing a hand to his shoulder as Shiro looked away in shame. "You did what you felt was best. Besides, if you didn't launch Unit-01's pod into space, Gendo could have gotten hold of it and done much worse with your soul and Unit-13."

"Yeah, I guess your right…. Speaking of Unit-13, how is it and the Mark.06 and 09 holding up?"

"Pretty good surprisingly. C'mon, let's head to EVA holding and we'll see them more up close." She stated, making her way towards the far side of the bridge. On the side they stood as was a flight of stairways next to the glass wall, connecting to the lower floor where the ship control stations laid. "After we got Unit-13, the Mark.0 and the mark.09 to safety we found you, Shinji, Kaworu Nagisa, and Rei Q all unconscious in your Entry Plugs. We had Shinji and Kaworu as you know taken to medical while Rei Q has been in the holding bay."

"That's weird. Has she done anything, tried to capture an EVA or something?"

"No, and even if she tried we removed all the Entry Plugs."

"Well that's good." Shiro said, gesturing towards the tram system at the back wall. "To tram I guess?"

"Yes." The pair quietly moved towards the small tram system, which consisted of a light grey triangular designed train that was held up by a set of wirings. The side of the tram housed a rectangular door, as well as windows and a large map of the ship. "So, what did it feel like?"

Shiro blinked, looking to Mana who stared back with curiosity. "What did what fell like…?" He asked slowly.

"You know… Being in an EVA and all….." Almost instantly, Shiro felt the temperature drop and he shivered. Mana easily saw his trouble look and felt worry brew in her stomach. "I, uh…. I mean y-you don't have to say it Shiro…. I mean…."

"It felt…. Warm…. And yet, cold simultaneously." Shiro honestly was at loss for words, because of in truth he didn't really know what it felt like. "I'm not sure… I was in an out during the time… It was weird…."

"I can tell…" She said, walking next to him. "You've actually got flesh and meat, no more metal parts…."

"Yeah." Shiro chuckled slightly. "Guess that's one of the good things about this huh?"

"I suppose." Mana replied with a small smile, before the train shuttered as it stopped. Above the door frame read a line of text 'DESTINATION: EVA HOLDING BAY.' "Here we are. Ready to see your giant robot body and weird... mom... clone old man Shiro?"

"Haha, very funny..." He replied sarcastically, doing what little he could to fix his hair before the tram door opened. "Yeah, I'm ready. Ready as I'll ever be."


	12. Rewrite Announcement

_**Okay…. I admit, I apologize for pulling a Hideaki Anno for God knows how long regarding EVA: We Can (And Will) Reverse This. Luckily for you all I won't wait two more years or more for the next chapter, as I have a important announcement for you all (If you haven't already read the title).**_

 _ **I plan on rewriting the story starting on Monday the 31st. Now, I've been rereading the story, reviewing what I've written and done Fanfiction wise (I.E EVA You Are (Not) Null and the original unedited chapters for We Can (And Will) Reverse This and have decided to alternate many things to the story.**_ _ **There's just too much**_ **this** _ **, too little**_ **that** _ **and a whole bunch of** **other stuff that make me ask "What as I thinking?" sometimes.**_ _ **And the reason I've been so quiet is because well… (Deep inhale) I've been watching and reading several other animes and manga's!**_

 _Ever reader: (pulls out pitchforks and torches) What?! Boo! How could you betray us?! You Bastard!_

 _ **Now before you pull out pull out your pitchforks and torches and all sorts of any other weapons of war, no I haven't given up on Evangelion or anything like that far from it I'm writing and waiting for the teased new movie coming out in 2020 so hell yeah!**_

 _ **Anyways, I plan to rewrite the story, and you'll already start seeing changes even in Chapter 1, but I'll mostly keep the story and ideas similar.**_

 _ **So yeah…. Again sorry for the extremely long Hiatus I've put on; been watching and doing a lot…. Still trying to buy all the Tokyo Ghoul and Re Manga's…**_

 _ **But anyways, I'm going to start rewriting once this goes up.**_

 _ **That said, this is the KnightOfZ3R0 signing off!**_


End file.
